That One Boss/Role-Playing Game/Pokémon

Behold the tales of Pokémon bosses, Gym Leaders, and Grand Masters for whom lolz at the player's expense flow more readily than the water in the Eclo Wastes. Keep in mind that due to the nature of these games and how they revolve around the player customizing their own team of Pokémon, difficulty of each boss can vary from player to player.

Generation I: Red, Blue and Yellow, plus FireRed and LeafGreen

 * Misty's Starmie would qualify since it's effectively an OU strong Pokémon fighting against unevolved Pokémon. Starmie is guaranteed to be faster and stronger than anything you will have at that point and it does very high damage even for mons that resist Water. It lacks a Psychic attack, but doesn't even need it.
 * It Got Worse in FireRed and LeafGreen, where her Starmie has switched BubbleBeam for Water Pulse which confuses you about once every three turns it's used. As we all know, if the opponents use a move with an effect, it will almost always instantly activate. If your Pokémon gets confused, it's more than likely to hit itself and faint in the process, which means that if you're hit with confusion, you may as well reset the game and avoid a lot of trouble by starting the match over again. Even with a Grass type at your disposal, this thing is very likely to trip them up with confusion, and their attacks don't do a huge amount of damage anyway.
 * Lt. Surge was fairly easy in Red and Blue, but in Yellow he became a monster. His Raichu is level 28, which towers over anything else you've faced. Speed? It goes first. Offense? STAB Thunderbolt will massacre anything in its path, and Raichu also knows Mega Punch and Mega Kick to take care of anything else, even the frail Diglett if you thought to be smart and use one. He has no other Pokémon, but why would he need any? It's a bit odd because in every other game he's in he's relatively easy because his Raichu doesn't have as many options against things like Diglett, but in this game he can be a nightmare.
 * Erika might not seem like much trouble. However, if she manages to get the first attack in, be prepared for her to spam the single most annoying attack of Gen 1, Wrap. Unlike the version of the attack you're now familiar with, Gen 1 Wrap prevented your Pokémon from taking any actions while they were caught. And guess what she'll do the moment your Pokémon is free from her Wrap attack? That's right, use Wrap again, preventing you from doing anything more than watching as the attack chips away your helpless Pokémon's health at a painfully slow pace to add insult to injury and God forbid she manages to paralyze your Pokémon while they're being Wrapped. You'll essentially be stuck in an infinite juggle. After the Wrap mechanics changed for the better in later generations however, she became a lot easier, managing to be somewhat annoying at worst.
 * Koga was annoying yet manageable in Red and Blue, but his Yellow team can be one hell of a surprise for unsuspecting players. His team is full of Venonat that have their levels grow higher in the forty range, ending with a Venomoth at a whopping level 50. At a point in the game where your own Pokémon are going to be in their mid/late 30's at best. If you don't have a way to reliably one-shot this overleveled Mothra-wannabe, then prepare for pain: it loves to spam Double Team while applying Toxic, slowly killing your Pokémon with steadily increasing poison damage while you can't lay a finger on it. Even worse, the only move with perfect accuracy back then was Swift, an underpowered move that likely won't be able to knock out his Venomoth before it knocks your Pokémon out.
 * He's back to using his reasonably leveled Koffings, Muk, and Weezing in Fire Red and Leaf Green, but at the cost of being much more unbearably annoying to deal with. Koga's two Koffings both know Self-Destruct which will K.O. anything lacking good bulk or a resistant typing, and every Pokémon of his will use Toxic while using Smokescreen and Minimize to make themselves harder to hit! And thanks to the fact that the Koffing family now has the ability Levitate to make their Ground weakness an immunity, you can't cheese the fight with a Ground type anymore. Even worse, his Muk knows Acid Armor, sharply raising its defenses so it can stay in the fight.
 * Sabrina in Gen 1 was easily the hardest boss fight in the game, bar none. A lot of it was thanks to how ridiculously broken Psychic types were: they had effectively no weaknesses thanks to the fact that the only damaging Bug moves were all horrifically under-powered and carried by the middling Beedrill, who would be obliterated by one Psychic or Psybeam thanks to its Poison subtyping and low speed. As for Ghost types? The only Ghost line in the game is part Poison as well, and the only damaging Ghost move is also pathetically weak, and it doesn't even matter thanks to faulty programming as Psychics are immune to Ghost moves! And thanks to the fact that her Psychic types (Especially Alakazam) had ridiculously high Special stats that combined Special Attack and Defense, they could tank Special hits for days while obliterating your guys with Psychic. And since speed was tied to critical hits, expect her ace of an Alakazam to get tons of critical hits. And even worse? Her Pokémon are on par with Koga's in Yellow, making her also ridiculously overleveled. She's a lot more reasonable in later generations since the Psychic type has long since been rebalanced, but keep in mind though that her signature move in Gen 3, Calm Mind, can crank her team's Special stats to frightening levels, so KO her Pokémon fast.

Generation II: Gold, Silver and Crystal, plus HeartGold and SoulSilver

 * Whitney starts off easy, and begins her gym battle by sending out a Clefairy that'll barely register as a speed bump (unless it rolls a devestating move with Metronome). But that's just false hope that her best Pokémon will gleefully crush under her hooves: Miltank. She has an attack called "Rollout" which gets stronger on subsequent use, and if it gets rolling, you're dead. And assume death is imminent should you have picked Cyndaquil for your starter, who's weak to Rock-type attacks. She has Attract, which will stun your male pokemon 50% of the time (bear in mind that male Pokémon are usually more likely to appear than female, depending on the species). She has Stomp, which is a strong attack (at least at the time you'll be facing her) that can flinch your Pokémon. So you finally got her down to red health? Miltank's got Milk Drink, which restores nearly all of her HP. This song sums it up nicely.
 * Upped to truly ridiculous levels in HeartGold & SoulSilver. Catching a Gastly to nullify Miltank's physical attacks doesn't work anymore -- they gave her the ability "Scrappy" (how appropriate) which allows her to hit Ghost-types with Normal-type attacks. On top of that, they gave it a Lum Berry as a hold item, so inflicting a status ailment on it will just make it heal itself. Sure, you can inflict the status a second time and it'll stick...assuming the status-inflicting Pokémon survives a second turn. At least Whitney's two Pokémon have dropped one level in the remakes. It doesn't help that much, but it does mean slightly less in each stat.
 * This is even referenced in the anime, where Ash takes Whitney on in a 3-on-3 battle, and Miltank takes all three of his Pokémon out in one Rollout, getting so strong that she deals a One Hit KO to them, and Ash loses the match. This is not only possible in the games, it's downright probable.
 * And it's not like the devs didn't know Whitney would be trouble, because they definitely did: the female Machop named Muscle that you can get from a trade in Goldenrod City's Department Store is specifically designed to counter her Pokémon due to being a female Fighting type, making her immune to Attract while STAB Karate Chop will, in theory, murder Miltank thanks to the type advantage. She's still not a safe bet thanks to five deadly words: "MILTANK used STOMP! MUSCLE flinched!" It's not very often that a boss will shit all over the thing specifically made to counter them, but it can and will happen.
 * In Gen II's remake, Bugsy can qualify for this if you're expecting him to be a pushover thanks to specializing in the Bug type. And indeed, his Metapod and Kakuna are insultingly easy, but he has a hell of an ace to make up for them: his Scyther. She has great stats for a Pokémon that isn't fully evolved, and can put up a hell of a fight thanks to Fury Cutter which gets stronger the more it hits, kind of like Rollout. Even then, Scyther in the original games is nothing compared to how tough she is in the remakes. She now carries U-Turn, a 70 power move that will switch her out with Bugsy's other team members, and if she's the last 'Mon standing, she can spam it with no repercussions. And thanks to carrying the Technician ability, her normally weak Quick Attack is much more powerful, which is a problem given that it's a priority move. Add in Focus Energy in order to raise her critical hit ratio, and this raptor mantis from hell can give even Rock types trouble if they whiff their attacks.
 * Remember how sending out a Gastly never works? Well, to be more precise, you sending out a Gastly never works. Meet Morty. This guy has Gengar, which is what Gastly eventually becomes when you've actually bothered to train it instead of backtracking, picking it up and hoping its immunity to Normal- and Fighting-type attacks will magically do away with the trouble you're having. Some exact stats for this species of Pokémon: Speed -- don't bother, he'll move first unless you inflict him with paralysis; Special Attack -- you may now start crying as it's fantastic. Before you manage to exploit his weaknesses, Gengar will in all likelihood hurl Shadow Balls at you until you die or use Hypnosis to put you to sleep. Then he'll hit you with Dream Eater, one of the most powerful Psychic-type attacks in the game. Refer to that thing's Special Attack stat from earlier and note that half the damage dealt will heal Gengar. Figured you'd switch out? Nope, he knows Mean Look. If that pathetic sleeping wreck over there having its dreams munched on was your only hope of defeating Gengar you'll have to use a Revive. Which at that point of the game is a strategy that will bankrupt you.
 * Gengar is far worse in the remakes by means of Gen IV's physical/special split. Shadow Ball is FAR more hurtful at this point in the game than it has a right to be. And all his Pokémon have Levitate in the remakes as well. So if you thought you were smart because you remembered that you can get Dig in National Park... too bad, it doesn't work against him anymore!
 * Chuck uses many variations of the Focus Punch strategies (some that are used by many competitive battlers) to make him terrifying. His horrifying Primeape in HG/SS will spam Double Team, then Focus Punch you to death. And he's pretty fast as well, and carries Rock Slide in order to counter any Flying types you bring in. His Poliwrath also makes use of these strategies: he can use Hypnosis to leave your Pokémon completely helpless due to sleep, then follow up with either Mind Reader and Dynamic Punch (Dynamic Punch is powerful and always confuses, but is very inaccurate, Mind Reader makes Dynamic Punch always hit) or Focus Punch (Very, VERY powerful more that won't be pulled off if the user is hit, though if you're asleep, it's a non-issue) depending on if you're playing the originals or the remakes.
 * Clair, the 8th gym leader from Gold/Silver/Crystal/HeartGold/SoulSilver. What makes her bad is The Ace of her team. Gyarados and Dragonair exist only to make you feel like you can win. With 3 of her Pokémon down she brings out Kingdra, a Water/Dragon-type you will grow to hate. You know that Ice attack you used on the Dragonair? Neutral damage. That Electric attack you beat Gyarados with? Neutral damage. The only attacks that are can score a super-effective hit are Dragon attacks... a department in which you're seriously lacking. She gets STAB on Dragon Pulse and Hydro Pump (both powerful moves) and, if she gets a critical hit, her Sniper ability ups the power bonus from double to triple. Then Clair has the gall to not give you the badge after you survive hell.
 * It's arguably just as bad, if not worse, in GSC. Not because she had three Dragonair, but that she would use Kingdra to spam Hyper Beam. And back in the day, Hyper Beam was codeword for: you're screwed. While she didn't have Hydro Pump or Dragon Pulse and instead had the weaker Surf and Dragonbreath, Hyper Beam more than made up for them, and they're not too shabby on their own. This is especially apparent with Dragonbreath as it had the high chance of inflicting your Pokémon with paralysis.
 * Do you remember the Kimono Girls? You know, the laughably weak trainers each using an easily-beaten Eeveelution back in the original Johto games? Well, they have taken not just one level in badass, but several in the remakes. Now instead of being fought early in Ecruteak where you could fight them in any order you wanted and didn't even need to do so until later, they are now fought after Claire in a boss rush, and their Eeveelutions now have proper movesets to wreck you with. Of note is Naoko's Espeon which fires off ludicrously powerful STAB Psychics and can copy your stat boosts with Psych Up, as well as Sayo's Jolteon which LOVES to spam Double Team before nailing you with equally powerful STAB Thunderbolts, and also has Thunder Wave for instant paralyzation. It should be noted that your rival specifically warns you about how tough they are, and boy oh BOY you better take him seriously when he says this.
 * Bruno of the Elite Four in the remakes has a Machamp with No Guard, which allows him to still hit your mons even if you use a move like Fly or Dig. And his moveset includes moves like Cross Chop and Stone Edge, which are both pretty powerful and normally innacurate, but no longer need to worry about that due to his ability. If you can't take Machamp down in one shot, this behemoth will wreck you five ways to Sunday. It should also be noted that his Hitmonchan can actually be a viable threat in these games thanks to the fact that Hitmonchan's hilariously weak elemental punches that ran off his pathetic Special Attack stat before now go off of his respectable Attack stat, and thanks to his Iron Fist ability which increases the damage done by punching moves, they will hurt.
 * Karen of the Elite Four in HG/SS. Her Houndoom's speed is VERY hard to match. Once she's set up with Nasty Plot, your annihilation is really a matter of choice: either she'll flinch you with Dark Pulses or roast you with Flamethrowers, both STAB-boosted, guaranteed to slaughter half your team. She's also packing an incredibly annoying Gengar that packs Destiny Bond which will take your Pokémon that KO's her down with her as well as an Umbreon that is obnoxiously tanky.
 * Remember Sabrina from higher up on the page? Yeah, she doesn't let up for GSC / HGSS either, as her Espeon will wreck you if you let it pull off a Calm Mind. Doesn't help how FAST that thing is, either. And her Alakazam is VERY FAST and LETHAL, and will easily KO most Pokémon you send after him. And he has Recover to restore his health. Do you think you are saved if you try to defeat him with a Dark or Steel Pokémon? Continue dreaming, he has Focus Blast, a Special Fighting attack with a power of 120.
 * Dark and Steel at least walled her a bit better in GSC, due to Focus Blast not existing yet and her mons in general not having as many move options available yet. But if you played GSC and then came into Heart Gold or Soul Silver expecting that... Espeon will be a pretty nasty surprise.
 * Blue in HeartGold/SoulSilver. Your team will be nerfed by Exeggutor's Trick Room, making the slowest Pokémon move first. The Mighty Glacier aspect of Pokémon like Machamp and Rhydon is thus conveniently removed, allowing them to destroy you. Of course, if you choose to rematch him, he turns out to have gotten a Tyranitar. Uh oh.

Generation III: Ruby, Sapphire and Emerald, plus Pokémon Omega Ruby and Alpha Sapphire

 * Brawly is the second gym leader you face in the game, and this guy hits hard. In Ruby and Sapphire, his first Pokémon is a Machop that knows Leer to lower your defenses, Bulk Up to raise his attack and defense, as well as Karate Chop and Seismic Toss, two fairly strong moves for this early in the game. Then Brawly sends out his Makuhita. He may look like a fat Pikachu, but don't underestimate him - this thing packs a wallop. First of all, he knows a move called Knock-Off, which does damage along with, you guessed it, knocking off your Pokemon's held item, making it unusable. He also knows Sand-Attack, which lowers your Pokemon's accuracy and makes your chances of hitting him insanely low. However, Arm Thrust is what you need to really watch out for. It is a move that can attack for up to five turns, and Makuhita spams this move in spades. To top it all off, he also knows Bulk Up, and will gladly increase his stats for you.
 * And in Emerald, his Makuhita knows the super-powerful Vital Throw, along with Reversal, which is a move that returns the same amount of damage that you do him. So get that puppy into the red zone and you are in for a world of pain. Thankfully, Sand Attack and Knock Off were taken out of his moveset.
 * Thankfully, his Pokémon's levels were lowered considerably in the remakes which in turn makes Brawly a lot more tolerable. However, he has his Makuhita packing Knock Off, which will hurt you if you think you can cheese the fight with a Ralts. While he had this move in the original Ruby and Sapphire, it was a Special move going off of Makuhita's godawful Special Sttack stat, while in this game it's physical, buffed considerably, and will probably one-shot the poor thing. Oh, and Sand Attack is back as well.
 * Wattson, especially in Emerald. He uses four Pokémon, all of which know Shock Wave, an attack that NEVER misses. Plus, all of his Pokémon get STAB on it, essentially turning it into a Thunderbolt with perfect accuracy. His various Pokémon have moves like Selfdestruct, a sacrificial attack that is five times as powerful than the standard Quick Attack (and that's without the fact that it halves the defense of the target in Gen 3); Rollout, a move that becomes more powerful after every successful hit; Thunder Wave, an ability that quarters a Pokémon's speed and makes it unable to attack half the time; and SonicBoom, a move that ignores-type effectiveness and can destroy any opponent in two or three hits. The fact that his Magneton is resistant to most attacks and his powerful Manectric evolved early a-la Falkner's Pidgeotto add insult to injury. And as Marriland would show you, god help you if you're doing a Nuzlocke run. Even moreso if you didn't pick up a Mudkip as your starter. Thankfully, Gen 6's rebalancing of Steel types, easier access to super effective moves, and the complete neutering of his team by making their movesets weaker and removing Manectric make him far easier in the remakes.
 * Flannery, mainly for her Torkoal. You obliterate her Slugmas and are feeling fine. But then comes the Demon-in-a-Half-Shell Torkoal, which promptly melts you with Overheat, makes it to where your male Pokémon can't do anything with Attract (consider yourself lucky if your lead Pokemon is female), and Body Slam to paralyze your Pokémon as well as deal some good damage. Then Flannery decides you still haven't had enough and uses Sunny Day, so all her attacks are 1.5 times as powerful now. Sure, Overheat causes a sharp stat loss whenever it's used, but this Torkoal is carrying a White Herb, which restores her stats. Oh wait, how about you lower her stats beforehand in order to make her use up her White Herb? No dice kid, her ability White Smoke prevents you from dropping her stats. Even worse: her supporting teammates carry moves like Sunny Day and the Screens, meaning that if you don't drop them all in one hit, her Torkoal will be even harder to defeat while her Overheat becomes ruthlessly powerful and Water moves will cease to do anything to her.
 * In the remakes, Flannery's Torkoal no longer carries Attract... but swapped it out for the deadlier Curse. With Curse, Torkoal will buff up her Attack and already monstrous defense to ridiculous levels, making her nigh-unkillable on a physical standpoint and boosting Body Slam's damage output. The worst thing is, Torkoal is already slow as molasses so the speed cut isn't even a drawback for her!
 * Norman. This guy is only the fifth gym leader, yet he has two Slakings, which have the highest attack stat of any non-legendary Pokémon up to then and a ton of HP. Even though they can only attack every other turn, they are still capable of KOing a Pokémon in one hit. He also has a Vigoroth, which is less powerful but pretty fast, able to attack before most other Pokémon you probably own, and isn't crippled by Truant. Finally, all three Pokémon come equipped with Facade, an attack that doubles in power if the user is poisoned, burned, or paralyzed. So if you're trying to break him with stuff like Thunder Wave, he'll just throw attacks at you that are only 10 points weaker than a Hyper Beam; and that's not counting the bonus Slaking gets from being the same-type as Facade. Norman is so tough in Ruby and Sapphire that when they updated all the Gym Rosters for Emerald he was the only one to get nerfed -- he still has Vigoroth and a Slaking but the other Slaking is replaced with Linoone and Spinda.
 * What makes him even more difficult is that his Pokémon are the standard 4-5 levels higher than the last Gym Leader, the usual. However, every other Gym Leader in the game is always several brand new routes away, giving you plenty of never-before-fought trainers to train your Pokemon against. Norman? He's waiting back at the 3rd town you went through, before you even had a single badge to your name. No new areas (besides a small stretch of desert), pitifully weak wild Pokemon, and the game expects you to be able to deal with Norman's power level.
 * And his Spinda in Emerald has Teeter Dance. Sure, he's pretty easy to knock out, but if you don't knock him out quickly enough for whatever reason, prepare to knock yourself out due to getting confused. And let's not forget also that his Linoone packs Belly Drum, which will max out his strength while cutting his health in half. He basically goes from a decent but non-threatening ComMon to a lightning quick death machine.
 * In Omega Ruby and Alpha Sapphire, Norman is even worse if that's possible. Why? Well, he has his old team of two Slakings and a Vigoroth back... and they all know Retaliate, fellow Normal type Gym Leader That One Boss Lenora's signature move. After you KO one of his Pokémon, Retaliate goes from a base 70 power to a base 140 power, meaning that you're going to have to eat attacks that are juuuuuuust weaker than a Hyper Beam. And to make things worse, his strongest Slaking knows Swagger, meaning that he can seriously mess you up even during the turns where he's loafing around. Since Swagger beefs up your attack power and causes confusion, your Pokémon will knock themselves out if the RNG decides to flip you the bird.
 * And there's also Winona in Gen III. Every member of her team knows Aerial Ace, which always hits. Her Altaria knows Earthquake and Dragon Dance. Once she gets off a couple of them, the blue bird becomes nearly untouchable and hits like a train.. Even worse: if you thought you'd be smart and slap Thunder/Thunderbolt on an Electric Pokémon and go to town on her team? Her Altaria has a Dragon subtyping that isn't readily obvious to a new player since its pre-evolution Swablu is Normal/Flying, meaning that Electric moves will hurt her for neutral damage and in return, your Electric type will be slaughtered remorselessly with Earthquake.
 * Good news everyone! Her Altaria no longer carries Dragon Dance in the remakes. However, she becomes annoyingly, ANNOYINGLY resilient thanks to carrying Cotton Guard to boost her physical defense to ridiculous levels while she has Roost to heal and lose her Flying subtyping. She won't sweep you anymore, but she WILL be hair-pullingly annoying to take down.
 * Tate and Liza in Emerald, which doubles as a very nasty shock to anyone who played Ruby or Sapphire. In Ruby/Sapphire, the only Pokémon the pair had were Solrock and Lunatone which meant that a Surf or two was enough to cream them. In Emerald, you first need to fight through a Xatu (which can either use Confuse Ray on your fighters or Calm Mind to jack up his stats, aside from flat-out attacking with Psychic) and a Claydol (which spams Earthquake and Ancientpower). If you do manage to get through those two, you'd think Solrock and Lunatone would be pieces of cake, right? Nope. It's not uncommon for Xatu to use Sunny Day before biting the dust, so Solrock can either hit with a powered-up Flamethrower or skip the charging turn to attack with SolarBeam Did I mention Claydol has STAB Earthquake, which hits every other Pokémon on the field and which the other three Pokémon on the Leaders' team are all immune to?
 * They return to using only Solrock and Lunatone in the remakes, but be careful as they receive one hell of a level jump, with their Pokémon both hitting level 45, while you've been fighting Pokémon that were five levels lower at the highest up to this point, and not even Archie or Maxie have Pokémon quite that strong. And because Surf also hits your ally in Gen 6, friendly fire will make you think twice about trying to beat them that way.
 * In Ruby and Sapphire, the last gym leader is Wallace, who is easy save for his Milotic. But if you are playing Emerald... good luck. Wallace is replaced by his mentor Juan, and he takes a page out of Clair's book by starting off with hilariously weak Pokémon that make you think you have a chance, only to spring a Kingdra on you. He has the ability Swift Swim, meaning that while it's raining, outspeeding him is nigh impossible, and that's on top of the rain boosting the power of his Water moves. He also uses the obnoxious Chesto-Rest strategy, allowing him to fully heal his HP and remove status at no cost (but only once; of course, after that once, Juan is all too happy to use Max Potions when his Kingdra's HP gets low). Did we mention Kingdra also has Double Team? Have fun with that.
 * Glacia gives players quite a hard time with her Walrein. She knows Sheer Cold, which WILL drop your Pokémon in one shot if it hits, which it probably will thanks to AI hax, and is very unlikely to be dropped in one hit thanks to her ridiculous bulk. And, in Emerald, her first Sealeo knows Encore! Wanted to do a quick buff to your stats? Whoops! Now you're stuck spamming that move while getting smacked in the face with a blizzard! She makes the upcoming Drake look pathetic in comparison.
 * Thanks to the later changes in Hail mechanics, Glacia becomes a lot more annoying in the remakes. Four of her five Pokémon know Hail, which is weather that will slowly chip away at any non-Ice type Pokémon's health. Annoying, but tolerable. However, her team can exploit it to the best of their abilities: her two Froslass become hard to hit thanks to their Snow Cloak ability upping their invasion in health, while one particularly annoying Froslass will mess you up with Confuse Ray and will try to get all of her stats boosted with Ominous Wind. And let's not forget: Hail makes it to where Blizzard never misses, so her Froslasses and Walrein can hit you non-stop with the 110 base power Blizzard without suffering from its shaky accuracy.
 * As to be expected, Steven puts up one hell of a fight as one would expect a champion to do. His starting Skarmory can stand up to Physical attacks for days while he sets up Spikes to hurt any switch-ins and will badly poison your Pokémon with Toxic. His Claydol is annoyingly bulky and will spread that privilege to the rest of his team by setting up Reflect and Light Screen. His ace, Metagross, is a pseudo-legendary with fantastic stats all around and will murder you with high powered moves like STAB Meteor Mash and Hyper Beam. And if his annoyingly tanky Cradily gets lucky with Ancientpower? ALL of his stats will increase, and make him a much bigger problem than before. To make things worse, his Pokémon tend to have good coverage with moves like Earthquake if you thought you'd be cute and sweep him with a Blaziken.
 * And in Omega Ruby and Alpha Sapphire, his Metagross can mega evolve. Mega Metagross has the ability Tough Claws which will make all contact moves hit MUCH harder. And surprise surprise, most of his attacks are contact moves, and he has it packing Bullet Punch so he will get the first hit in if needed. It's not uncommon for players to handle the rest of his team considerably well, only to be completely obliterated singlehandedly by Mega Metagross.
 * If you were expecting to fight Steven as the champion in Emerald and thus loaded up on Fire and Ground types, Wallace can be a nasty surprise when you see him waiting for you in the Champion's room. Even if you didn't he can still put up a hell of a fight: his wall of a Tentacruel will whittle you away with Toxic while boosting his defenses to insane levels with Barrier, his Ludicolo lacks either of Water's weaknesses to Grass and Electric and will annoy you to death with Double Team antics, and his Milotic is generally built to last, can hit decently hard, and will poison you with Toxic. And if his Gyarados can get off a Dragon Dance, kiss your whole team goodbye as that thing will tear you apart and WILL kill any Electric types with Earthquake.
 * For players of Omega Ruby and Alpha Sapphire, Primal Groudon and Primal Kyogre are quite easily the nastiest legendary mascots you ever have to fight in the main series of video games. Their old abilities Drought and Drizzle have been replaced with Desolate Land and Primordial Sea which are the former abilities on steroids. This is especially the case with Primal Groudon, as its ability makes it completely immune to any and all water moves, and Primal Kyogre is no slacker either as Primordial Sea makes its already powerful Origin Pulse absolutely terrifying, and will tear off huge chunks of health from even Pokémon that resist it. And if you thought that catching them would be a piece of cake like with Reshiram and Zekrom as well as Xerneas and Yveltal in Black/White and X/Y? Nope, because unlike those four, they have the typical ludicrously low Legendary catch rate which makes them nigh-uncatchable even at one health while afflicted with a status condition, even if you're using the right Pokéball for the job. And even lowering their health is a chore in and of itself, as Primal Kyogre packs Aqua Ring to gradually restore its health while Primal Groudon has Rest to not only instantly restore its health completely, but also remove any status conditions as well. Many 3DS's have likely been smashed by furious players that succumb to the wrath of these ancient abominations.
 * And speaking of tough legendary Pokémon, we have the final boss of the Delta Episode of Omega Ruby and Alpha Sapphire which makes it the final boss of the games as a whole,
 * The Battle Frontier in Emerald is, as a rule, much harder than anything the main game will throw at you. The enemy Pokémon you'll be fighting will be packing ideal natures, EV's, IV's, and movesets with plenty of coverage. If you want to beat any of its facilities, you'll need to have top-tier competitive level Pokémon and intimate knowledge of competitive gameplay. However, some of the Frontier Brains are ridiculous, even by this place's high standards.
 * Palace Maven Spenser. In general, the Battle Palace saddles you with the frustrating gimmick of having to let your Pokémon fight on their own without player inputs, and whether they'd use ideal moves or even attack at all is essentially up to luck. So naturally, the boss of such a place is designed to be about as fun as dragging your balls through broken glass. He starts off with a Crobat that will wear you down with Toxic and do everything in its power to make sure you never land a hit. It'll use Confuse Ray to trip you up, spam Double Team, and use Fly to make it impossible to hit at all for one turn. Somehow get past that, and you have a brutally powerful Slaking and a Lapras with Quick Claw and Horn Drill to look forward to. And that combination is infamous for ending many a run of any Battle Frontier facility: thanks to the stupidly unfair way enemy luck is blatantly boosted the more you win, it's not uncommon for a player's run to end because a Pokémon's Quick Claw activated every turn and let it move first regardless of your guys' speed, and never miss a single Horn Drill, which is normally inacurrate to hilarious extents. Thankfully, Crobat and Lapras are gone in the rematch... but you still have to deal with his Slaking, and Lapras is replaced with a Suicune packing a dangerous Special Attack-oriented moveset and Calm Mind to boost its power. If it manages to use Calm Mind even once, then get ready kiss your winning streak goodbye.
 * Salon Maiden Anabel doesn't rely on any tricks or gimmicks, she's simply a skilled opponent with great Pokémon. The first time you fight her, she's tough but not overly so, but during the rematch she pulls out all the stops. She's packing two Olympus Mons in the form of Raikou and Latios respectively, and they're both specially-inclined hard-hitters who will beef themselves up with Calm Mind while Latios is holding Brightpowder that can make your moves more likely to miss. And her last Pokémon is a Snorlax, a tanky competitive powerhouse that will boost its Attack and Defense with Curse, then pound your 'Mons into dust with Return and Shadow Ball. You better hope you have a way to bypass its defenses and kill it fast because it has Rest to heal itself with, and is even packing a Chesto Berry so it can immediately wake up and attack the first time it Rests.
 * Pike Queen Lucy is another gimmickless battle, but the tradeoff is that your Pokémon are very likely to be wounded or hit with crippling status effects thanks to the Battle Pike's luck-based gimmicks. Thankfully her signature Seviper isn't all that strong (though if it pulls off a Quick Claw/Swagger combo, you're in trouble), but her other Pokémon make up for it: her Shuckle puts the "Stone" in "Stone Wall" and will not die thanks to its fortress-tier defenses, all the while whittling your team away with Sandstorm and Toxic while using Rest to recover all its health. Beat it, and you've essentially got a rematch with Wallace's powerful Milotic to look forward to. Thankfully her Shuckle is replaced with the inferior Steelix in the rematch and her Milotic is also replaced with a Gyarados that can't even touch your Ghost types thanks to having the Normal type Return as its only attack, but she's still not to be underestimated: her Seviper is now guaranteed to get off a Swagger thanks to its Focus Band allowing it to survive a fatal blow, and if you don't have a Ghost type, her Gyarados will happily sweep you with its Dragon Dance-boosted Return.

Generation IV: Diamond, Pearl and Platinum

 * Fantina was tough but manageable in Diamond and Pearl, but she became a nightmare in Platinum. Her first two Pokémon aren't anything special, but her Mismagius is a force to be reckoned with. When she was the fifth gym leader, Mismagius was a decently powerful speedy Special Attacker that ultimately wasn't that big of a deal, but due to being demoted to third gym leader in Platinum, that witchy ghost now a ludicrously powerful Special Sweeper with stats that make her a terror against your team of early-mid level Pokémon. She has Shadow Ball which is incredibly powerful by itself, but even moreso due to STAB bonuses. There's also Psybeam which is very likely to confuse you, and Magical Leaf, which never misses and provides coverage against any Water, Rock, and Ground types you may have. And to top it off, she has Confuse Ray which is guaranteed to confuse you assuming Psybeam didn't do the job. Mismagius had these exact same moves in the original games, but in Platinum, Fantina's earlier placement makes all the difference in the world.
 * Maylene in Diamond and Pearl is a real threat thanks to her Lucario. He has fantastic stats to start with, and has a typing that eliminates Fighting's weaknesses to Psychic and Flying in the form of Steel/Fighting. Thought that one of Sinnoh's two Fire types could exploit that Steel typing's Fire weakness? The multi-hitting Ground move Bone Rush will be a nasty surprise. And even worse, DP era Sinnoh has some down-right lousy diversity issues with Pokémon, giving you considerably fewer options to take down that monster with, an issue mitigated by Platinum having a much better selection of Pokémon.
 * Cyrus, especially in Platinum though he's no pushover in the originals either. Gyarados used Waterfall! Bam, you're dead. Reload. Gyarados used Earthquake! Bam, you're dead. Gyarados used Ice Fang! Bam, you're dead. In Platinum, his Gyarados has a Quick Claw. So even if you have an Electabuzz, Magneton, or something really fast with an Electric attack, he might get you before you can slam him.
 * The rest of his team doesn't let up either. Thought you could tank his Honchkrow's Dark and Flying moves with a Steel type? Nope, time for a surprise Heat Wave! Thought you could cheese his newcomer Houndoom with a Water type? He's packing Thunder Fang, so think again! And his Crobat will annoy you to death with Confuse Ray and Toxic antics while his Weavile can hit hard in general and has Brick Break in case you thought you could wall him with a Steel type. Seriously, all of Cyrus's Pokémon in the Distortion World pack great stats and movesets, making him one of THE hardest boss fights in the game, if not the series.
 * Cyrus isn't the only hard Team Galactic member, his Admins Mars and Jupiter are unforgiving in their first battles. Both of them each have early access to Glameow and Stunky's evolutions Purugly and Skuntank. And by early, we mean levels 16 and 23 when they normally evolve at 38! Not only are they quite bulky and hard hitting for when you fight them, but Skuntank is especially a pain thanks to her carrying the powerful Night Slash, which has a high critical hit ratio and can be a guaranteed one-hit KO against your Pokémon if your luck is bad. Their Zubats also have access to some pretty gnarly moves like Giga Drain to surprise your Rock types with, and Toxic to induce bad poisoning way earlier than what you're used to.
 * Their double battle on Mt. Coronet is just awful, though. Thanks to your rival starting with a bulky Munchlax that does nothing but spam Stockpile and Swallow (And lacks anything resembling killing power thanks to being a baby Pokémon), it just uselessly sits around with its thumb up its ass while you basically have to fight a double battle by yourself against their Pokémon who love to gang up on yours. To save yourself from an obnoxious fight, just kill his Munchlax first so Barry can actually send out a helpful Pokémon in his stead.
 * Flint. So you're geared up with your Water, Ground, or Rock-type Pokémon, ready to stomp those Fire-types of his. But then you find out that three of his five Pokémon aren't Fire-type. The Infernape was outright terrifying due to its high level and great coverage (Flare Blitz, Thunderpunch, Earthquake, and Mach Punch). Platinum was much nicer to us about it, though, giving him a full team of Fire-types.
 * He usually starts off with Sunny Day, and then the "fun" really begins. His Infernape's Flare Blitz combined with Sunny Day will pretty much instantly defeat anything that isn't resistant to Fire, or immune to it in the case of Pokémon with the ability Flash Fire, and even then he still knows Earthquake to take care of them.
 * He's still no slouch in Platinum though. He has a full Fire-type team now, but he will make your life miserable if he can use Sunny Day to set up the sun. Your Water Pokémon will cease to one-hit KO his Pokémon while they get Solarbeamed to death, and let's not forget about his Magmortar's fantastic coverage with Thunderbolt as well, and like Cyrus he also has an annoying Houndoom with Thunder Fang.
 * Let's not forget Lucian, who directly follows Flint in the Elite 4. He's a Psychic-type user, and his team is nasty. Mr. Mime using reflect and light screen will stop your one-shots. Then there's Alakazam, with huge speed and special attack, then there's his Bronzong. Remember that little Bronzor that kicked your butt before? Meet its big brother. Its type combination already limits your options, but then throw in a Levitate Skill to axe the omnipotent Earthquake attack. Oh, and it can throw Earthquake at you too. In Platinum, his ace is now a Gallade which is both Fighting and Psychic, meaning that if you expected to have an easy fight with a Dark type, you're in for a bad time.
 * What makes this battle even worse is that in Diamond and Pearl, not only is Bronzong 4 levels stronger, but the severe lack of Fire types in the Sinnoh region pre-National Dex (the only ones are the Ponyta and Chimchar lines), so if you started with Chimchar, Bronzong can counter that with Psychic for most likely a 0HKO, and Rapidash has relatively sub-par stats save for its speed, so good luck doing noticeable damage. Oh, and the aformentioned Earthquake will still be an issue.
 * The champion battle with Cynthia is by far one of the most difficult fights of the franchise. Her team is very highly leveled even compared to the fight immediately before her, has varied types, and boasts perfect EVs and IVs across the board, meaning that they're far stronger than normal Pokémon you'd fight at the same level. And even worse, each individual Pokémon has the potential to be a threat on their own. Her Dark/Ghost Spiritomb has no weaknesses to any types since Fairy was not a typing back then, you just have to have a mon strong enough to hit her until she faints while you run the risk of her getting all of her stats boosted with Silver Wind. Her Milotic is annoyingly tanky and will turn any special attacks you use back on you with Mirror Coat while she carries Ice Beam to fight off Grass types, while her Togekiss in Platinum is incredibly obnoxious with fantastic coverage moves Water Pulse, Shock Wave, and Aura Sphere to compliment Flying STAB Air Slash. Her Lucario, Roserade, and Diamond/Pearl exclusive Gastrodon are easier, yet still hit very hard and all pack at least one coverage move in order to handle types they are weak to (Stone Edge for Lucario, Sludge Bomb for Gastrodon, and Shadow Ball for Roserade, though only for Diamond and Pearl). And then there's the crown jewel of her team, Garchomp, a monster of a Pokémon that is so utterly overpowered Smogon banned it from its competitive play rules altogether during the 4th gen competitive metagame. (And the fifth gen metagame as well, despite the power creep.) This nasty land shark can very well solo your entire team, and even having an Ice type doesn't mean you necessarily win, as she's carrying Flamethrower to roast them.

Generation V: Black and White

 * Gen V follows the tradition of Normal-type Gym Leaders being That One Boss with Lenora. Her Watchog knows Retaliate, a Normal-type move with a very respectable base power of 70. However, if a Pokémon in the user's party faints on the same turn, it doubles to a whopping 140, and that's not even counting STAB. Since Watchog will always be Lenora's second Pokémon, she can Retaliate right after you defeat Herdier, and she can OHKO pretty much anything you throw at her. It doesn't stop there, either. Her Watchog knows Crunch, a very powerful move at that point in the game, and can put your Pokémon to sleep with Hypnosis. Herdier is no pushover either, having stats comparable to Watchog's and knowing Take Down, which hurts a lot coming from a Normal-type.
 * Her successor Cheren is just as bad in the sequels. He's the first gym leader, and he uses Patrat and Lillipup as his Pokémon, so you'd expect him to be easy, right? WRONG. His signature move is Work Up, which boosts both of his Pokémon's attacking stats. While his Patrat is easy enough to take out, his Lillipup is bulky for this point in the game, so you're pretty much doomed once he starts fighting back after a few Work Up boosts. And to make things worse, unlike Lenora who you might at least be able to handle easier with Fighting moves, there is no way to have a Fighting type move at the point of the game Cheren is in, even if you have a Riolu! Unless of course, you either want to rely on hoping it will survive a boosted Tackle and one shot it with Counter, or grind like hell for a fighting move way past Lillipup's level.
 * We also have the fourth Gym Leader, Elesa. She uses two Emolga (Electric/Flying) and one Zebstrika (Electric). Her two Emolga are immune to Ground and know Double Team, and literally nothing will be super effective against them because you won't have any super effective moves for Emolga (unless you caught a Roggenrola, which is very slow) at that point in the game — even worse, one of the trainers you meet before her also has an Emolga. Then her Zebstrika is so fast and so strong that she mows down anything that gets in her way. And all three get Volt Switch, which does respectable damage and switches them out against anything that isn't Ground. Thankfully, she only has one Emolga in the sequel that you will be prepared for since Gamefreak got the memo and have Clyde the Guide specifically warn you about that Pokémon. Her replacement, a Flaafy who loves to spam Cotton Guard is still irritating to fight, though still not quite as bad as two Emolga.
 * And in Black and White 2's challenge mode she now carries a truly nasty surprise in the form of Joltik with Energy Ball, which will murder any Ground types you'd try to bring in.
 * Elesa even has the dubious honor of coming after another That One Boss: N. Or more specifically, his Sigilyph, which has insane stats for that section of the game - his Speed is high enough to nearly guarantee him the first strike against anything you throw at him, and he knows Tailwind to eliminate the "nearly". His Special Attack is high enough to virtually guarantee a One-Hit Kill on pretty much any Pokemon that doesn't resist both his Psybeam AND his Air Cutter. Think trying to resist both Electric and Flying is a nightmare? Trying to resist Psychic and Flying may well be even harder. Think he's a Glass Cannon? Not at that point in the game it isn't. Want to try wearing him down with Poison? Don't bother, he has Magic Guard. Burn doesn't work either, as all his attacks are Special.
 * If your Pokémon happen to be kinda slow, Clay's Excadrill will likely wipe out your entire team thanks to his ridiculous attack stat and fantastic moves to compliment it. Even worse, he has the mole packing Hone Claws which increases Attack and Accuracy, making his moves hit ludicrously hard and undodgeable. Add the fact that all of his Pokémon carry his signature move Bulldoze which lower the victim's speed, and you can see how bad things can get with him. It's worth noting that your Rival Hugh in the sequels will specifically warn you about the upcoming battle, and you better heed it with a vengeance.
 * Even within the Elite Four, Marshal can be pretty difficult because all his Fighting-types have very high attack stats and are capable of taking a hit. His Sawk has Sturdy, which keeps you from OHKOing him while he can dole out the punishment. Throh has big HP and will likely not be taken down without you receiving a big hit in return and packs Counter to wipe out your physical hitting Pokémon that fail to one-shot him. His behemoth of a Conkeldurr packs Stone Edge to cover his Flying weakness and is powerful enough to one-shot a lot of what you throw at him. Most players consider him to be the toughest member of the Elite Four, and for good reason.
 * Shauntal can be a pain considering most of her Pokemon have a secondary type, meaning that they're actually somewhat well-balanced in comparison to other Elite Four members and have access to STAB Water, Fire, and Ground moves to surprise you with. In particular, her Chandelure is incredibly fast and can roast your Pokémon with ridiculously powerful special attacks while her obnoxious Cofagrigus is a wall that will whittle your own Pokémon away. Even worse, Chandelure is carrying a Choice Scarf in Black 2 and White 2's Challenge Mode.
 * The Final Boss can be a real hair-puller, coming immediately after another difficult fight without so much as a chance to save - thankfully your Pokémon are healed fully between the fights, but this is still a trick the franchise rarely pulls. Some of his Pokémon are more deadly than others; Bouffalant is a juggernaut with his powerful STAB Head Charge and amazing defenses, Eelektross is an Electric Pokémon with Levitate (which means no weaknesses) and has the offensive stats to do more than stall. But that's just preparing you for his worst: an underleveled Hydreigon. This thing is monstrous. Aside from the fact that he's almost certainly a couple levels above you, he has astonishingly good type coverage. Thought you'd throw that legendary you just got at him? Guess again, he'll massacre it with STABed Dragon Pulses. Okay, so you'll try Ice. Now he's either melting it with Fire Blast or shattering it with Focus Blast. Finally, if you can whittle him down,   tends to use a Full Restore right before you can finish it off. Despair Event Horizon is right through that door.
 * This is made even worse by the fact that it has been found that the EV's and IV's of Hydreigon are actually maxed, meaning that the stats for that specific Hydreigon cannot go any higher at the level he's at without in-battle buffs. This means that Hydreigon can decimate Pokemon up to ten levels higher than him since its stats are far beyond standard for its level, making it one of the toughest bosses in the franchise.
 * In the sequels, is actually MUCH easier than he was in the original games, surprisingly. However, there's still an incredibly hard boss among the ranks of Team Plasma in the form of Colress. He uses a Magneton, an already solid special attacker that holds an Eviolite, which makes it annoyingly bulky. His Magnezone is also pretty bad due to carrying Thunder Wave and is even better at Special Attacking thanks to being Magneton's evolved form, and both Pokémon can NOT be taken down in one move thanks to their Sturdy ability. His team also has Pokémon among it's ranks such as a Calm Minding Beheeyem and a Gear Grinding Klinklang. All in all, Colress is one tough son of a bitch to take down.
 * Champion Iris (also from the sequels) is no slouch either. If you were relieved by how hard underleveled Hydreigon has fallen from grace, she makes up for it with an underleveled Hydreigon of her own. Like the one  used in the original games, she has fantastic type coverage as well as Charge Beam, which boosts her Special Attack to high levels as well as doing damage. To make things worse, it's her first Pokemon, meaning that Iris is more than capable of sweeping your team right out the door. And if you do take Hydreigon out, the rest of her team is quite competent. Her Lapras is a bulky Pokémon who can put your team to sleep with Sing and runs Thunderbolt and Ice Beam for amazing coverage, her Aggron is physically tanky, her Druddigon is hard hitting, bulky, and carries a Life Orb to hit even harder, and her Archeops is both ridiculously powerful and lightning quick to boot (Unless his health gets below half, thank GOD for the Defeatist ability). Then there's Haxorus, her ace-in-the-hole and your scariest opponent yet. She already has a ridiculous Attack stat, but she also packs Dragon Dance which makes she faster AND even more powerful! And because she's packing a Focus Sash, you can't KO her in one hit. You basically have to hope and pray with all your might that she doesn't use Dragon Dance, because if she gets even one under her belt, your fate is sealed.
 * So you've beaten Black and White and are feeling great. You're slowly leveling your team up even higher in preparation of fighting the Pokémon League properly, and make a pit stop in the beachside Undella Town. It's a peaceful tropical paradise, so you decide to hang around for a while and explore. You head inside the nearest house... only to find waiting for you.

Generation VI: X and Y

 * While X and Y are notorious for being among the easiest games in the series, they still pack their fair share of tough bosses, the first one being Gym Leader Grant. He uses Rock types, so like Brock and the other Rock type gym leaders, he'd be easy right? Wrong. DEAD wrong. His Amaura is a very bulky little Pokémon that has the refrigerate ability, which turns Normal moves into Ice ones, meaning he now gets STAB off of the already powerful Take Down, and will paralyze your Pokémon with Thunder Wave. Then, there's his Tyrunt, which has a Dragon subtyping that will remove a few of Rock's common weaknesses. He's also very powerful in general, as he has STAB Rock Tomb to do decent damage and slow you down, Strong Jaw-boosted Bite, and Stomp, which will proceed to flinch you to hell if your speed drops below Tyrunt's. Needless to say, Grant almost more than makes up for the amount of very easy Gym Leaders by himself.
 * Siebold of the Elite Four is often considered by many to be the hardest opponent in the game, and for good reason. His Water type team is full of incredibly good Pokémon, with Gyarados being a stand-out example, as he can become a speedy sweeper thanks to Dragon Dance, and he has Earthquake and Ice Fang to eliminate Water's common weaknesses. And even with that one out of the way, his other teammates don't let up. His Clawitzer has fantastic coverage in the form of Aura Sphere and Dark Pulse, moves that are boosted by his Mega Launcher ability. Starmie, meanwhile, is an incredibly fast Special sweeper packing great moves including Dazzling Gleam for Dark type coverage, and his Barbaracle is an all around good Physical attacker.
 * Fellow Elite Four member Wikstrom is also pretty nasty. His Probopass packs lots of pretty decent moves and is impossible to drop in one hit thanks to sturdy, his Scizor packs the dreaded STAB Bullet Punch + Technician combo utilized by lots of competitive players, his Klefki WILL annoy with priority Spikes and Torment thanks to Prankster, and his Aegislash will either tank you completely, or utterly annihilate you thanks to his stance change gimmick.
 * Most of Team Flare isn't noteworthy, but Xerosic can be problematic. His Crobat is as obnoxious as you'd expect a Crobat to be, but his Malamar can be a real nightmare if he isn't dispatched right away. His main strategy is to hit you with Superpower, a powerful fighting move that usually lowers the user's Physical Attack and Defense, but raises them instead thanks to Malamar's Contrary ability. Thanks to constant boosts to its physical stats, he's more than capable of being a huge threat on his own.
 * The final battle with Lysandre is also fittingly tough. His Pokémon are all-around decent with high levels and great stats, but his Gyarados... or shall we say MEGA GYARADOS is more than enough to completely wipe you out. When his Gyarados Mega evolves, he gets a massive attack boost, and he has great type coverage to wipe you out with. He has Waterfall for STAB, Outrage as a fuck-off 120 power move, and Earthquake and Iron Head in order to cover his weaknesses to Electric and Fairy respectively (he gains a Dark subtyping upon mega-evolving, which would make Fairy a weakness... or not thanks to the aforementioned Iron Head).

Pokémon Ranger

 * Charizard in the first game. The second time with him is a lot harder. Not only does he like to fly around while blowing flames, but his fireballs scatter much more densely, making it hard to circle him -- and even with assists, it takes a lot of loops to get him. It also doesn't help that if you take too long, he flees the battle and you have to start all over again...
 * Several players have a pretty rough time with Steelix, too. Even when he coils up (which is about the only time that circling him is even possible), his sheer size makes drawing those loops awkward. Having multiple Water and/or Fighting assists comes highly recommended.
 * Drapion is a rather irritating boss due to the fact that you face two group captures directly before it. And that you come to a full stop at one part unless you happen to have a Normal-type Poké Assist ready.
 * Flygon. You're not allowed any other Pokémon because it's a "test" and the bloody thing resists Plusle/Minun's assists. And it's incredibly fast, making it nigh-impossible to get the amount of circles you need to finish the battle.
 * Entei. Not only is the whole thing a Sequential Boss, you have to deal with the fact that it basically attacks the entire screen. And in the refight, you can only bring three Pokémon for the whole thing...
 * Metagross can be a real pain if you don't have the right assists. It pretty much fills the screen with beams and makes shields for itself.
 * in the second and third games causes damage just by WALKING. It's easy to screw up and lose and assisting Pokémon, and your Styler gets damaged if you don't circle the thing immediately before or after it launches an attack.
 * Ditto in Guardian Signs. You thought fighting each of the beasts individually was bad, this thing will transform into each of them over the course of the fight. Unless you have a variety of Poké Assists, you're in for a long fight.
 * Feraligatr in the third game. It's not so bad before and after it rages, but while it's raging, it tackles all. the. time. And 9 times out of 10, it will charge off screen so you can't circle it between attacks, not that there's much time in between for circling it. And each tackle does 10 points of damage.
 * Salamence in the first game. Like with Flygon, you aren't allowed to have other Pokemon with you. Unlike Flygon, however, it's slow but more than makes up for it by having to draw a ridiculous amount of circles around it. It also outright ignores your starter's assist, and likes to fly above the battlefield for long stretches of time, meaning you can't circle it. Simply landing counts as an attack, and it hurts.

Other Spinoffs

 * Pokémon Colosseum's Cipher Admins; this isn't so much because they were difficult to defeat but because you had to spend ages trying to capture the legendary beasts while keeping yours alive. Don't forget the fact that, when you catch a Shadow Pokémon, all they have is Shadow Rush (at least in Colosseum, anyway)... but before you catch them, their original trainers can use all of their other moves. It also means that there's a chance that your Shadow Pokemon-owning opponent could use Shadow Rush, which gives recoil damage. This means that someone trying to catch a Shadow Pokemon had to be very careful about the opponent's HP; leaving it at 1 HP or near it could leave it vulnerable to its own recoil. At least the Shadow Pokemon owners generally didn't use Shadow Rush, but that doesn't mean the possibility was gone.
 * Miror B because he has several Ludicolo that have Rain Dance to activate their abilities Rain Dish and Swift Swim which will either regenerate their health or make them faster than you. Not to mention the fact that they are all fully evolved Pokémon that are at a decent level and have very few weaknesses you can exploit at that point in the game, and their water moves hit harder than normal thanks to the rain. Even more annoyingly so, his Ludicolo packs moves like Leech Seed and Mega Drain to constantly sap your health away with.
 * Dakim was far more annoying as you had to try to capture the legendary Fire Pokémon Entei, who was weak to Ground moves. Guess what Dakim's favorite move was? That's right, Earthquake! Every one of his Pokémon had it, and most of them got a STAB bonus from it as it hit everyone else on the field, which meant that if Entei came out too early, it was going to get knocked out before you could catch it. If their constant Earthquakes didn't defeat you, the high probability of Entei fainting too soon would probably have you replaying this fight over and over again. And in later fights, he packs a lot of Fire type attacks on his Pokémon as well as Sunny Day and Solarbeam, and will do Protectquake maneuvers while also firing off Solarbeams that require no charge times, and to make matters worse any Water types you bought in would be next to useless due to his sun!
 * Lady Venus of the Under combines That One Boss with Goddamned Boss quite effectively. To wit, her Pokémon are all nothing special by themselves, but they carry tons of annoying status moves to annoy your Pokémon with. ALL of her Pokémon except for Suicune pack Attract which will mess up any afflicted Pokémon of the opposite gender, and she's very big on stacking poison, confusion, and even the ghost type Curse on your Pokémon to keep the damage going. And in case if you thought you could fight back with similar tactics? Her Misdreavus and his Taunt will shut down any non-damaging moves you'd annoy her with. And in all subsequent battles after you've snagged her Suicune, it's replaced with a tanky, hard-hitting Milotic that will boost its defenses to ridiculous levels if you get her with a status move, meaning that the fight will become worse if you try to use her own strategies against her!
 * The fact that Ein loves to spam Toxic and Confuse Ray and have his Pokémon use Protect to wait out your Pokemon fall to the poison and confusion already should clue you in on how irritating his battle is, but he has another strategy on top of that to make the fight even worse. He's a huge fan of having a Pokémon use Rain Dance to not only boost their moves, but to help make it to where a Thunder coming from his Electric types will always hit. This strategy can tear your team to shreds if you're unprepared, and if you thought you'd be clever and try to use Thunder on his Water types instead, a few of his Pokémon such as Rhydon have Lightningrod to make sure you can't turn his own strategy against him!
 * The final boss, Evice, is pretty difficult, but generally par for the last boss of a Pokémon game. However, should his Slaking and Slowking end up on the field together at any point, you're screwed. Slaking's stats are equal to those of Groudon's. Slowking will use Skill Swap at the first possible chance, which gives it Truant and gives Slaking the ability to attack every turn. Say goodbye to any hope of beating it now. Even if you beat his two, he's still incredibly tough due to the fact that all of his Pokémon are bulky hard-hitters who will boost their attack power even higher. Of note are his Scizor who will Baton Pass Swords Dances to his other teammates, and his Salamence which is just ludicrously powerful in general. It should also notice that if you didn't take any time to grind, your Pokémon will very likely be at the high forties/low fifties while his Pokémon are all above level sixty! THat level jump really, really hurts.
 * The second fight with Snattle in Pokémon XD: Gale of Darkness also hurts quite a bit if you don't have the right number (or quality) of sweepers. Why? Starmie. It hits fast, hard, and if you haven't been dragging a tank of a Shadow Pokémon around to soak up the damage, it can wipe out an entire non-Shadow team. Its Shadow Solrock partner, by contrast, is almost insultingly easy after that thing.
 * And even when you win, Cipher Peon Kleef proves Dangerously Genre Savvy by ambushing your team as you go through the Door to Before, while the next healing machine is through him or another boss and the last one is a major backtrack. Thankfully Kleef is otherwise pathetic (a team of stallers with no Shadow Pokémon to snag) and XD allows saving anywhere, but it really hurts when your team has such major injuries.
 * Thug Zook, when encountered outside the Key Lair immediately after is a nightmare. He has a Shadow Zangoose with him that is above the typical level for that point in the game, and it will happily kill off one of your team members every single turn, first, without fail. Essentially this forces you to constantly pick away at it with the survivor, hoping you have enough firepower to kill it before it wipes out your whole team, and then proceed to spam Revives and healing items while his other Pokémon are busy trying to kill you less effectively. It's so bad that in the rematch with him, his mons haven't leveled up at all, and he's still a very hard opponent to beat.
 * Grand Master  can be this for the unprepared. Three Shadow Legendary Pokemon (the legendary birds) at Lv. 50+, plus another three relatively strong Shadow Pokemon (Exeggutor, Tauros, Rhydon) at Lv. 46+. What this means is that powerful attacks will be headed your way, and every attack against you will be super effective (Shadow attacks are super effective against non-Shadow Pokemon, but thankfully/possibly no same attack type bonus), as well as a low catch rate for the Legendary Pokemon. If you're not prepared, you'll run out of Revives and/or Snag Balls before all six can be snagged.
 * His right hand man is also incredibly difficult. He has four Shadow Pokémon, the highest amount you will have fought in the game at that point, and they're all quite nasty. Special mention goes to his Marowak, who hits ridiculously hard thanks to its Thick Club held item, and his Salamence, an incredibly powerful Pokémon that is at level fifty at a point in the game where you've been fighting Pokémon whose levels are, at the highest, in the mid-forites. And save for his Shadow Manectric, his Shadow Pokémon have a decent amount of bulk which makes whittling them down to capture even harder to do since you've got to deal with a never-ending volley of powerful, always super-effective attacks from his end.
 * Those bloody group bosses in Pokémon Mystery Dungeon: Explorers of Time/Darkness. I'm talking to you, Luxio/Electrike tribe,, 'The Grand Master of All Things Bad' and their cronies. And let's not forget.
 * Primal Dialga is no pushover either. He packs a lot of HP. He's got a great defensive typing (Steel/Dragon). He's got the intimidator IQ skill, which more often than not prevents you from hitting him at melee range. And to top it off, he's got Roar of Time, which can hit both you and your partners from anywhere in the arena, is surprisingly accurate and deals triple digit damage... at a stage when you just reached triple digit HP, which means you'll really need those oran berries and reviver seeds. Oh, and you fight in your unevolved forms and losing forces you to climb Temporal Tower again?
 * Pokémon Stadium 2 brings us Janine. She's easy in Round 1, but what's her strategy for Round 2? Baton Passing multiple layers of Double Team (a move normally banned in Smogon competitive play for being too luck-based). All her Baton Pass targets can take a few good hits, have Confuse Ray, Attract, or Swagger to screw with your chances of hitting even further, and will wear you down with Toxic and Sandstorm. If you're planning to just switch out, take note that she's also packing Spikes and Mean Look. She will slowly torture you to death unless you come prepared with Haze and Heal Bell, but even then you're still at the mercy of many elements of luck.
 * Erika had a really annoying rematch Vaporeon because of the former ruling that Sleep Talk could pick Rest again to restore the health. Vaporeon having a ton of HP and decent special defenses did not help matters at all.
 * Sashay from the "little cup" Sunny Park Colosseum in Pokémon Battle Revolution. Especially her Treecko. That stupid thing spams Energy Ball like there's no tomorrow. A big attack like that on a little baby is a big surprise for those who aren't prepared!
 * In Pokémon Battle Revolution, everyone becomes That One Boss on the "Level 50 -- Rank 8" setting. The boss of the Colosseum will throw uber legendaries at you just to screw you over. "Colosseum Leader Taylor sent out KYOGRE!"--cue rage quit--And it's not just the bosses! On rank 8, everyone leading up to the boss will use 3 legendaries at the very least. And don't even get started on Mysterial!