Beast Wars/WMG

For Wild Mass Guessing about the rest of the franchise, see Transformers.

Rhinox is actually Optimus Prime, just reformatted into a different body.
So, Optimus, sometime after the creation of Rampage, realizes that the Maximals are in many ways no better than the Decepticons and decides just to leave. Instead of killing himself, he simply gets a new body at the same time everyone else on Cybertron is getting one and starts a new life from there. This would explain his excellent leadership abilities and his very spiritual nature. It also leads up to his eventual betrayal in "Beast Machines". It's not that he hates organics, but more that he is tired of the violence and war that has plagued his race since their creation. He believes that he is the best to do this because he is Optimus Prime, the one and only.

The Decepticon Ravage sacrificed himself in Beast Wars not out of loyalty to his former commander Megatron, but to his pre-Cybertronian Wars Autobot friend Nightstalker.
Beast Wars is based on no one version of the G1 continuity. One issue of the European G1 comics showed Ravage, Optimus Prime, and Megatron before the dawn of the Great Wars, with Ravage the protector of the last planetary leader, with an Autobot counterpart named Nightstalker. Nightstalker sacrificed himself to ensure his lord lived, but Ravage let the old 'bot die, believing Megatron to be the planet's best chance for surviving the oncoming war. Ravage's death for Megatron's cause in Beast Wars is painfully identical to that of Nightstalker, and a comment by Magmatron in a Beast Wars comic hints that Ravage's first and foremost allegiance was to himself, a sentiment proven viable by his abandonment of his old Cassettacon comrades after their Predacon rebuild to become an agent for the Tripredacus Council, whom they were opposed to. Hence, the most likely reason for Ravage to sacrifice himself for his lord would be to make up for his betrayal of his friend so many millennia ago.
 * Also, Nightstalker lives in the form of Nitrostreak, an old buddy of Tigatron's. It's been shown many times that a Transformer blowing up isn't even close to confirming they're dead, so it's possible that he (barely) survived and was saved by Optimus. Furthermore, in the Timelines comic, a Maximal with Nightstalker's exact coloring named Nitrostreak is shown alongside a pre-Beast Wars Tigatron; Transformers generally keep a similar color scheme when they upgrade to a new body, their names are similar, and many of the other members of the team Tigatron and Nitrostreak are a part of are based on other Beast Wars or G1 animaloid Transformers. Thus, Nightstalker lives as Nitrostreak, ironically making Ravage's sacrifice moot.

"The Great Upgrade" in BW Era is just first step in Cybertronian and Humanity merging as a species
First off, let's start with reason for each races. Humanity: They wanted to expand from Earth, but lack serious technology and their fleshling selve are bit fragile in deepspace. Cybertronian: With the civil war and all, they found out that their species is dying en masse. They still have the need to revive Cybertron that require massive amount of energon, but at the same time, they needed the scarce energon to sustain themselves.

So, with the reason established, each race develops a method to merge with each other. Cybertronian, seeing that human's anatomy conserved much more energy and simply more nimble, decide to upgrade themselves by downsizing the overall size into normal humanoid size shedding the large frame. Human, also in a way, upgrade themselves to this form. But one question remain, the universe at large is largely organic lifeform. In the event of energon absence or depletion, they need to sustain themselves with organic material(i.e eating organic matter). Thus they begun the techno-organic project. This particular project's aim is to integrate Hardiness of metal technology and the organic diversity. As the project almost come to completion, Predacon/Decepticon faction decide that they like staying metal, and sabotage the project, destroying all the tech-org goop on Cybertron. Since all of humanity is either converted to metal or willingly turn themselves into tech-org material, the source of that project is lost aside from the record of humanity's origin, the Golden Disk featured in BW-era.

Blackarachnia gained telekinetic powers during her Transmetal II upgrade due to her mind link with Tarantulas.
Every other Transmetal II-upgraded Transformer in Beast Wars has enhanced abilities and precisely one new power: the power to use their spark to heal themselves. Blackarachnia had not shown any sort of psychic/ferrokinetic power before her upgrade, and the only instance of her coming into contact with psychic powers is when she mind-linked with Tarantulas. While telepathy is not telekinesis, they are both psychic powers, and are often grouped together in fantasy and Superhero comics. Therefore, one logical explanation is that the residual effects of the mind link were enhanced in the upgrade, to telekinetic proportions.

Scorponok and Terrorsaur are alive.
As has been said before: Transformers and lava, don't get me started.
 * In fact, look really close at Terrorsaur as he's sinking into the lava; he's glowing, indicating that he's undergoing Transmetalization at the time. The writers admit that this was done to give both 'bots an "out" of their deaths in the future, if they decided to bring them back.
 * Of course, just because they were alive doesn't mean they ever got out of the lava. Hopefully, they went into Stasis Lock quickly.

Rampage wanted Depth Charge to kill him all along.
After all, he was designed to be immortal, and even if he hadn't wound up twisted and monstrous and kept under lock and key, Rampage probably could figure out the downsides of living forever. Hence, when opportunity presented itself, Rampage directed his cruelty towards Depth Charge (it's already been established that Rampage has went on killing sprees where Depth Charge was present at least twice, and didn't kill Depth Charge either time) in the hopes that, wracked by grief and vengefulness, the Maximal would find a way to end Protoform X's theoretically-eternal life.
 * This can be supported by the fact that, when it came down to actual act, Rampage is shown letting go of the energon spike Depth Charge has poised above his chest.
 * An alternative possibility is that Rampage realized he was screwed, and he activated his kill switch mode as a result. This way, when Depth Charge stabbed him, all his weapons would detonate (which, considering he blew up a mountain with them, says something). Rampage knew DC would stop at nothing to kill him at that point, so he wanted the sadistic glee of knowing that DC would have to die to fulfill his quest.
 * Another possibility is that it was Rampage's final act of corrupting Depth Charge. After all, Rampage repeatedly taunted Depth Charge.
 * More likely, Rampage was seeking out death the entire time. Consider: the Maximal who became Rampage had been Spark-raped into becoming an immortal killing maching. His comment to Black Arachnia of "I regret everything" seems to imply that, while he is very good at what he does and a part of him enjoys it, he hates himself for what he has been turned into. Him letting go of the energon spike was him desperately hoping that he would finally be at peace.

Depth Charge was suicidal.
On the flip side, it's possible that Depth Charge's survivor's guilt lead to him seeking his own destruction. He was always going off by himself and taking on dangerous missions. Note that he didn't hesitate to kill himself in order to off Rampage.
 * Well, when he had the chance to get back to life (in one of the many comics of the Expanded Universe), he was pretty bitter about being resurrected.

The Maximal Elders are just as fanatical as the Predacons.
They've deemed Earth and other key G1 historical sites off-limits to everyone, keep historical records and information tightly controlled, experiment on their own citizens, and have a "separate but equal" racist standing with the "lower class" Predacons, the first three the Predacon ruling class has to our knowledge haven't done yet. Clearly, the Elders are so paranoid about another Great War that they're perfectly happy with Jumping Off the Slippery Slope and becoming tyrants themselves. Sure, the Preds are planning a rebellion, but at least they're smart enough (mostly) to bide their time and use the Pax Cybertronia to build up their resources without incident. They even genuinely oppose BW Megs' plans to use the Golden Disk to force Pred rule, which shows that they're not as "evil" and power-hungry as they seem.
 * Possibly such morals were passed to Optimus Primal, as he wanted to put Transmutate into stasis lock (read as euthanize) because it had power but lacked brains.

The Maximals left on prehistoric Earth eventually became the Battle Beasts.
It was never confirmed that the destruction of the Planet Buster nuked all of the stasis pods (and, in fact, with the discovery of Silverbolt and Quickstrike, Primal specifically orders Airazor and Tigatron to scout for more intact protoforms), so it's very likely that they cracked open into new Maximals and Predacons that were left on Earth when the Beast Wars were over. Of course, as shown in Beast Machines, it would take millions of years for them to get back to Cybertron on their own power, but there's still a lot of scrap left over from three ships (the Axalon, the Darksyde, and Ravage's stealth ship) to make their own sub-transwarp ship. It's possible that, if they left Earth, they ended up on another planet instead of Cybertron. Plus, there's the fact that the Battle Beasts are anthropomorphic Earth animals, decked out with cybernetics somewhat similar to Cybertronian technology, and the fact that their factions are broken up for the most part into the mammals and birds versus reptiles and insects (the same species split the Maximals and Predacons had during the Beast Wars), and you can pretty much connect the dots from there.
 * Two words: Primeval Dawn.
 * The statis pods only hold Maximal protoforms. Without someone reprogramming them, they would all be Maximals.
 * Technically, yes, but Quickstrike was bloodthirsty enough on his own to become a Predacon without needing a shell program. Other protoforms could be the same.

All of the Arthropod-based Predacons are Actually Female
Why? Because of the simple fact that their Beast Modes are female. Waspinator is a wasp with a stinger, which means that he's not a Drone, and therefore female. Inferno is a soldier ant, and also therefore female. Tarantulas has a larger rounded abdomen, and Rampage has big claws, both of which are telltale signs of sexual dimorphism among Arthropods. Scorponok and Quickstrike... well, honestly, does anyone even care either way? Granted, they don't have female personalities, but, being robots, there's no reason why their personality or even their physiology needs to line up with their gender.
 * Of course, this assumes that the "true" gender of a Cybertronian is the same as the physical sex of their altmode. This may not be the case; of course, what defines said gender is highly vague in every Transformers series.
 * I don't know where you got your tarantula knowledge, but a large rounded abdomen IS NOT a sign of a female tarantula. It's just a sign of a well-fed one. The only way to tell a male from a female involves a magnifying glass and weird structures on their underside. A sexually mature male frequently has a smaller abdomen due to losing interest in food, that's all. If anything, Tarantulas' altmode is male - his transmetal upgrade appears to have enlarged pedipalps (the little short arms near his face), a telltale sign of a mature male. (Yeah, I'm a nerd.)
 * They probably just have beast modes based on females.

Tarantulus was a Quintesson (or one of their agents).
Think about it: they'd have plenty of good reasons to want to off both Autobot and Decepticon while not being descended from them. They have a vested interest in reclaiming Cybertron (former Quintessonian factory). They hate the Transformers (they Turned Against Their Masters). They're sadistic perverts (watch The Movie). And not being gods or Sufficiently Advanced Aliens, they can't just do stuff through sheer will. Megatron's "Unicron's Spawn" was just an insult.
 * This makes perfect sense if you don't want the Unicron's Spawn comment to be literal in your personal canon. Tarantulas' scheme was especially audacious, but hardly unheard of for a Quintesson -- time and dimension travel were both technologies that the Quintessons were familiar with, and they had once tried to avert the Cybertronian Revolution by time-snatching the pivotal fighter, A3. We know from G1 that even after losing Quintessa, they frequently spied upon or otherwise interferred with Autobots and Decepticons alike. Furthermore, as the entities who built the first Cybertronians, surely they could make the perfect infiltrator agent? It stands to reason that they continued to spy on Cybertron long after the events of Season 3, and realising the Maximals and Predacons were losing their memories of the events of Transformers Generations One, began seeding Cybertron with secret agents, new Transformers built in their own labs designed to hide amongst the Cybertronians and work on whatever schemes their Quintesson masters commanded.
 * So, by extension, that means that the entire Tripredacus Council is composed by Quintessons...
 * Word of God states that the intention was for Megatron's comments to be literal; conflict among the writers, however, lead to the compromise of "Let them decide for themselves".

Maximal/Predacon bodies are descended from Micromaster and Pretender technology.
Pretenders were the first Transformers to have an externally-organic appearance. Over time, one can assume this technology was improved, going from an outer shell to an integrated part of the robot. Micromasters, meanwhile, are smaller, more fuel-efficient Cybertronians; with energy sources being the main source of conflict in the original series, having everyone take on such forms may have been not just a strategic decision, but a life-and-death necessity.
 * Possibly, this also involves Powermaster technology. This involved Transformers who used organic beings as power sources; among other effects, this allowed them to use alternate power sources -- such as food. Since Beast Wars characters are repeatedly seen eating...

Megatron's plot to destroy Optimus Prime while in stasis would have spelled doom for both races.
When the original Megatron put out the Golden Discs, he wouldn't have known about Unicron, so when Unicron finally decided to destroy Cybertron, there would have been no Matrix to stop him. So, BW Megatron's attempt to Screw Destiny would have resulted in a short-lived (from the perspective of Immortal Robots) victory for the Decepticons. Nice Job Breaking It Villain.
 * Megatron's ending in the Nintendo 64 game says, yes, this is pretty much what would have happened.
 * It also explains why Megatron held off on implementing that plan for as long as he did; he knew (or at least figured out) that, and attempted to find alternate ways of gaining Decepticon victory.
 * BW Megs waited because by the time he realized that, yes, they really were on Earth, he didn't have the disc anymore. Without the disc he couldn't locate and/or enter the Ark, much less do anything to the inactive bots inside. Between the Vok artifacts (with which he didn't need his original plan) he was pursuing throughout the second season and Maximal interference he didn't have the botpower to just search the whole planet, either.
 * Actually, BW Megs knew he was on Earth in "Code of Hero": with the Disc in hand, he mused that if it were not for the human race that sprang up from the valley, the Autobots would have lost. In addition, it is noted by Silverbolt and Blackarachnia that Megatron had previously dug a tunnel to the Ark, and then had it blasted shut.

Starscream's files were covered up because of Protoform X.
The Maximal elders only allowed the information that Starscream was immortal so they could justify making the spark. They conveniently left out the part where he was treacherous so they could got forward with the experiment, maybe in the hopes of capturing Starscream's original scientist persona back before the Great War.

Waspinator was manufactured by Acme.
Recipient (and survivor) of a great many Amusing Injuries? Check. Perpetual Butt Monkey? Double check. It explains so much.
 * This troper thinks that his spark lays in his head.

Megatron and Dinobot were more than just comrades-in-arms.
Given the vast differences between their personalities and belief-systems, it isn't immediately obvious why Dinobot would have joined the Predacons; Tarantulas was there for his enigmatic 'missions,' Waspinator and Terrorsaur because they were easily cowed, Scorponok was dead loyal to Megatron, but Dinobot was there because he and Megatron jointly founded the expedition, a plan which grew out of their relationship. The reason why Dinobot ditched back in episode 1-1 is because at that point they were already in conflict, philosophically and because Megatron -- with his 'anything for the cause' attitude -- wasn't remaining exclusive. Probably with Scorponok, hence why he was the first to blast Dinobot. This explains the Megatron images in Dinobot's computer (more specifically, the speed with which he clicks it shut when he's disturbed; c'mon, you know the feeling) and Megatron's repeated Dinobot clones. When you can't be with the one you love, make inexplicable copies of him. The reason why Dinobot defected back in Maximal, No More wasn't really the whole 'clash of honor' thing, it was the fact that Inferno's behavior towards Megatron meant that, once more, Megatron wasn't exactly pining.
 * Either that, or the relationship was one-sided, and Dinobot was either oblivious or deeply disturbed by Megatron's interest. Dinobot was genuinely interested in what Megatron was trying to do (or what Megatron told him, which likely was along the lines "use golden discs to get massive energon source on Earth and take over Cybertron in glorious combat, since he didn't seem aware of Megatron's "Kill Optimus Prime" mission)
 * Oh, he knew: "Your insanity will destroy us all, Maximal and Predacon alike and all those who came before." Uttered in Maximal, No More. Of course to further complicate this guess, Dinobot couldn't follow Megatron since he'd had to kill Rattrap. Sure, he could slag the future, but still his would-be rival? Perish the thought.
 * Or Dinobot was just smart enough/familiar enough with Megatron to put the pieces together once he had all the information.

Dinobot joined Megatron's crew knowing he himself would die.
There can be little doubt Dinobot knew he was going to die a few episodes before he did, from the lengthy speeches to uploading a copy of himself and even confirmation from his VA: According to McNeil, Dinobot knew he was going to die five episodes before he did, as right up until the last second, he believed Dinobot to only be "cartoon dead" as opposed to "dead dead". However, what if Dinobot knew from the beginning that he was fated to die by sacrificing himself to save humans on earth, and THAT was the reason he join Megs, in order to test his fate himself. This could be a reason behind his berserker and at times suicidal nature. This, in addition to Dinobot's knowledge of Megatron's plans to disrupt history on Earth (RT: "Where have you been, out saving the universe?" DB: "Possibly", (paraphrasing) DB: "Your plan proceeds", "Megatron is near a great victory", "Your plans will destroy all who came before", etc) adds fuel to the fire when Dinobot confronts Megatron about being on the wrong planet in the first episode, the need to defeat him at any cost, and later, Dinobot's obsession with fate and the need to be the master of it ("For I could not live if not the master of my own fate!").
 * Possibly, conditions of his death were recorded on the Golden Disc itself, as evidenced when Dinobot is in his quarters at the beginning of "Maximal, No More" analyzing the Golden Disc against Megs' plans.
 * Could it be that the Maximals that witnessed DB's death had something to do with this? Do they make a time traveling stop on the way home and inadvertently spread the word of his good deed, which then gets recorded onto the Golden Disc or someplace else?

Tarantulas wasn't worried about the meddling with the Ark not just because his origin lies with Unicron, but because he's not even from this universe.
Before he reformatted into a Predacon, Tarantulas was a universe hopping motorcycle by the name of Sideways.
 * Both Tarantulas's cybertronian mode and his transmetal vehicle mode are motorcycles.
 * Tarantulas is a sneaky, treacherous backstabber, like Sideways.
 * Sideways possesses supernatural powers, like Tarantulas.
 * Tarantulas and Sideways have both shown a measure of immortality.
 * When have Transformers not shown some measure of immortality?
 * Optimuses dies fairly easily, although making it stick is the tricky bit.
 * So, they Live Forever outside of getting slagged, and even that doesn't necessarily stop them. Again, I reiterate the question :).
 * Tarantulas was slagged but uploaded his mind into Blackarachnia. When his body was repaired, he was transmetalized. Since his spark was never transferred bodies, it's more likely he used the Trans-Phase mode used by Sideways.
 * The Animated Allspark 2 suggests that, even further, he's also Animated Sideways and Revenge of the Fallen Sideways, via black hole/timeloop/something.

Waspinator is immortal
While all Transformers are hard to kill, Waspinator is on a whole other level. He gets mangled and dismembered worse than even Rampage, and late series he stops even bothering with stasis lock. Waspinator doesn't automatically self repair like Rampage, but neither did Starscream.
 * At some point they say "Mutant" Indestructible Spark. Which means that, technically it can manifest at random. So Waspinator is a mutant like Starscream. This means any cybertronian can have one, but its probably incredibly rare.
 * Another thing I noted is that "immortal" Transformers are all a bit insane. Starscream is very cowardly yet completely obsessed with power. If he was sane, he would have simply given up after failling again and again. (Dinobot sorta gave up after one or two episode). Starscream seems to have a "glitchy" compulsion to betray. Rampage is psychotic AND treacherous. Waspinator is also anormal. His speech pattern and whacky personnality are side-effect of his immortality.
 * Waspinator was possesed by the mutant immortal spark of Starscream, making him the ONLY one (within Beast Wars anyway) to have been 'used' in such a manner. This experience may have given him an edge in the not-dying game.

The same thing which happened to the Maximals could have happened to the Predacons as well.
I'm talking about the episode Call of the Wild, where Megatron and co. stole the Energon Dampener from the Axalon, making the base vulnerable to the energon, and thus, forcing the Maxies to remain in Beast mode until the wilderness of their beast modes take control of their system. Dinobot (a Pred working with the Maxies) was affected as well. Dinobot was a Pred. A pure Pred. Even when he worked with the Maxies. So... both Maximals and Predacons are vulnerable to all the same things.
 * Inferno wouldn't have been affected. Like Tigatron and Airrazor, he's pretty in-tune with his Beast Form.
 * It's possible that the predicons had already went through the same thing. Inferno and Tarantulas already seemed far too in touch with their beast modes to begin with and most of the others would have been held up enough by the problematic terrain inside the predacon base for things to get too out of control. I wouldn't be surprised if Megatron managed to fall into the CR tank and then forced the others to snap out of it. This would have also explained how he knew what would happen.
 * Megatron said that he knew it would happen because he had researched Maximal programming.

Tarantulus infected Megatron with a virus that turned him into a Manchurian Agent
...on behalf of Tarantulus' master, Unicron. The trigger, of course, was returning to Cybertron, and the action was a feeling of hatred for organics and to wipe out the population. Unicron wanted the initial plan- assasinating the Matrix-bearer at his weakest- to succeed, but on the off-chance it didn't, wanted a backup plan that would result in Cybertron (and thus Primus) being rendered defenseless. Megatron and the Maximals taking him to justice were actually just Unwitting Pawns. This is why his behavior changed so drastically in Beast Machines.

Megatron did not suffer Character Derailment, only Character Development...
... partly off-screen. By the end of Beast Wars, Megatron had already become consumed with hatred for organic life (particularly primates) and obsessed with godhood. However, he still was a rogue, a Neutral Evil madman with Chaotic Evil tendencies. However, when he broke free of his bonds during the Transwarp journey to cybertron and landed earlier than his captors, he was able to use his manipulative talents, significant Transmetal 2 powers (Optimal powers, perhaps?), and his lust for ultimate power to take over Cybertron, with the help of his engineered plagues. As he plotted his future vision of Cybertron, it became less and less chaotic, less organic, more concerned with order and perfection. Thus, Beast Machines Megatron was no different from Beast Wars Megatron. Just older.
 * In Master Blaster, Megatron wanted to take the original Megatron's spark into himself in order to gain the immense power of Optimal Optimus. Instead of becoming a technological Jet-Truck-Monkey, he was reformatted into an almost entirely organic dragon. The jealousy over their differences helped fuel his later hatred for organics.
 * The hatred of organics was probably enhanced by the fact that, in order to take advantage of the new powers he developed on Earth, he would have to remain in the mostly-organic Transmetal II form. On a technological cybertron. No doubt he encountered enough prejudice due to how different it made him- and how difficult it would have made rule by charisma- to make him hate organics in general.

The episode The Low Road has a Meaningful Name...
...and it was on purpose. Just think... Dinobot and Rattrap going on a subway road to retrieve a spark... and then... Rhinox and his fueled Weapon of Gas Destruction.

Dinobot is descended from the Dinobots
First of all, that's where he got that name from. It was passed down, not because he was going to pick a dinosaur form on Earth. Secondly, that's why he had so much honor and courage despite being a Predacon. However, he did have some Decepticon ancestry, thus explaining why he wasn't fully good until, and why he was a Predacon to begin with.
 * According to IMDb, Dinobot is descended from Grimlock, so this could be true.

Dinobot (II) is still alive.
This isn't even a wild guess. Think about it, when the Nemesis went down Dinobot still had half of a mutant immortal spark inside of him. Short of having a chunk of raw energon thrust into it I don't see how he could have NOT survived.

Rubber Ducky was, in fact, a Predacon, and was The Man Behind the Man giving instructions to Megatron.
He was smart enough to want to not be known, which is why he faked non-sapience whenever there was a chance of being seen or heard; Megatron consulted with him and recieved orders and strategy offscreen. He was also the level-headed sane one of the group, explaining why Megatron went completely off the deep end in Beast Machines- without his boss giving him orders, he had to rely on his own prejudices and intellect. This is also why Megatron was so good at manipulating, keeping tabs on, and seeing through the Xanatos Gambits of the other Predacons- the real one in charge was small enough and unassuming enough to be a perfect spy, and he simply figured out how to turn what he saw to his favor, and relayed that to his figurehead.
 * Things rather went south after he was annihilated by Tigerhawk though...

Beast Megatron was planning to take G1 Megatron's place in history after destroying the Ark.
He was already carrying G1 Megatron's spark so his personal ancestry would have been protected from the timestorm made by the Ark's destruction. He would then travel back to Cybertron in the Nemesis without time traveling and take command of the Deceptacons during the Great War. Using his knowledge of history and the lack of Optimus Prime, Megatron would quickly end the Great War long before the events of G1. Then Megatron would prepare Cybertron to defend against Unicron, which Megatron also knows is coming. After that Megatron would recreate the beast wars in order to complete a Stable Time Loop that would maintain his control over Cybertron.

Cybertron was experiencing an Energon shortage when Megatron stole the Golden Disk.
It's canon that Maximal and Predacon forms were designed to be more fuel-efficient than Autobots and Deceptacons, which shows that the leaders of Cybertron anticipated a shortage of Energon. Exploration ships like the Axalon would have been paid a finder's fee for any Energon deposits discovered, which is why Rattrap signed up for exploration. Current Energon reserves were being severely rationed on Cybertron to the point where any promise of more Energon would be enough for Megatron to recruit a crew. When the Axalon disappeared the Maximals only sent unmanned probes to search for it, which used minimal amounts of Energon. The Tripredicus Council assumed Megatron had already found Energon and built refineries for it so they sent Ravage without enough Energon to get back and expected him to refuel there. Had the Vok not destroyed most of the Energon on Earth the planet would have become the Middle East of Transformers.

The Beast Wars are responsible for bringing the Great War to Earth.
The Planet Buster came within seconds of destroying the Earth with no evidence of temporal disturbances, which means the Ark hadn't arrived yet. The Ark detected the transwarp wave and came to Earth to investigate the origin of it, where it was promptly shot down by the Nemesis before any scans could be made.
 * There wouldn't be any effect unless history deviated from what was supposed to happen. Earth only had one moon in the future, and nowhere near as much energon, the planet getting blasted was always supposed t happen.

The Vok are the Ultimate evolution of the Spiral Races.
The Vok's goal is stated in the expanded universe to be guiding other species to higher evolutionary levels. Despite their... odd methods of ensuring success, they may be attempting an all-out war against the Anti-Spirals. That, and they seem to select "heralds" of their own to restore order AND allow all beings in the universe to live peacefully without the Anti-Spirals threatening to kill them. Swindle was right; they really ARE nice creatures.

The Insecticons from G1 gained their beast modes and amnesia due to Tarantulas's attempts to alter the past.
When the Insecticons first appeared in the original Transformers cartoon there were several questions regarding their origin that were never answered. They apparently came from a Decepticon escape pod that had been jetisoned from the Nemesis, and after some prompting from Megatron, seemed to vaguely recognize him and their faction but they lacked any concrete memories of their past. Also, their alternate forms were capable of digesting organic matter and turning it into energon, an ability that is treated by the Decepticons as being unique.

We know that Tarantulas was working to rebuild the Nemesis. It's possible that during his search for the ship he discovered the Insecticons and sought to repair them using technology from his time period, hence why the Insecticons have beast modes and are able to convert organic matter into energon, an ability that the Maximals and Predacons have been alluded to have. (We have seen them eating in beast modes on several occasions, and in "The Low Road" Primal outright told an infected Rhinox to eat something in order to keep his energy levels up.) Tarantulas also sought to alter their minds to serve him, perhaps with a Predacon shell program, but due to differences between past and current Transformers technology, which had previously been seen when Teletraan-1's shielding failed to interface with technology from the Axalon in "Go With the Flow," the shell program failed and instead wiped the Insecticons' minds.

Rhinox wasn't as nice as he seemed
He was just acting so nice because he was stuck in a situation where his personal opinions weren't relevant. Notice just how evil he became in "Dark Designs", then also notice just how little Blackarachnia's personality changed when her programming changed from Predacon to Maximal. Was it the reprogramming that made him so nasty or was it merely an excuse? We've seen that Maximals are not inherently good, Quickstrike was never reprogrammed and was a sadistic monster and even Rattrap was quite a selfish jerk a lot of the time. In the fifth episode, after Optimus was absorbed by an alien probe, the Maximals vote between Rattrap and Dinobot as new leader, a vote that somehow ended up a tie. Both bots clearly voted for themselves and Cheetor was far too optimistic to vote in favor of Dinobot's harsh, merciless methods which would mean that Rhinox was the one that voted in favor of Dinobot. He's also the one that insists that the vote was secret after Rattrap demands to know who voted for Dinobot, with Cheetor showing no reaction to the accusation. Notice how after Optimus' death Rhinox asserts leadership with pure force? It would place his characterization in Beast Machines as him merely saying "Screw it" to playing nice as their world was slagged anyway.
 * The evidence is in favor of Cheetor voting for Dinobot (http://www.youtube.com/watch?v=-2Mmc8W58og). Remember that this episode was not long after Dinobot was the only one to treat Cheetor like a respectable adult and Cheetor never did figure out that it was blatant manipulation. And Rhinox does clap Rattrap on the shoulder to congratulate his victory. He likely insists the votes remain secret out of respect for proper democracy, although he knows darn well who voted for Dinobot by simple process of elimination.

Predafied Rhinox was still working for the Maximals
The tech used to convert him was described as increasing his aggression. But aggression is not the same as loyalty. Rhinox was still loyal to Optimus, but he was playing along with Megatron's plans. To better screw him.

The Megatron named in the Covenant of Primus was Megatronus Prime, The Fallen
The "-us Prime" suffix was removed to represent his Fall. The Hero who would not win but would not surrender was one of the other Primes, as was the Mighty Warrior with the rainbows. The great mountain rising from the sea refers to a hidden unicronian ship underneath the Sea of Rust on Cybrertron, and the bit about "they who live and war as beasts" was just it being derrogatory about unircronian followers acting cruder and being doomed to death at the hands of righteous bots. The similarities are just coincidence, or Primus intentionally making the thing apply to multiple events- the Beast Wars aren't the last circumstances it will describe eerily as history repeats over and over.
 * This editor has held this to be personal canon ever since the reveal of Megatronus Prime's identity, with the caveat that because the Covenant of Primus is weirdly prone to providing unexpected humor, that the use of "Megatron" was a typo from Megatronus, meaning it was the only usage to survive the find-and-replace of "Megatronus Prime" to "The Fallen".

Cheetor was a grad student
Its easy to forget, but the Axiom was a research vessel, and the crew of four active (Optimus, Rhinox, Rattrap, and Cheetor) were scientists. That's easy to believe for Optimus and Rhinox, and Rattrap may not have the personality, but he is clever and intelligent enough, just socially crude. Cheetor, however, has the personality and intelligence of a child, especially compared to the other three. What is somebody young and naive doing on a research vessel? He's obviously a graduate student coming along to do basic grunt work, learn about whatever they were working on by experience, and maybe write a basic thesis about it.

Tarantulas was not a Spawn of Unicron. He was actually a Paradronian

 * Paradron was a Cybertronian colony that fled Cybertron and settled on a new world of their own in "The Fourth Great War", one of the many Cybertronian Civil Wars before that fought by Optimus Prime and Megatron, and which was destroyed during the Civil War fought between Rodimus Prime and Galvatron. Presumably, many Paradronians would have felt hatred of both the Decepticons who forced their planet to be destroyed and the Autobots for actually destroying it -- or just the fact that even millions of years after Paradron was settled, their "cousins" still couldn't figure out how to get along, which cost them Paradron. Cue bitter, resentful, grudge-bearing "nu-Cybertronians", passing down their negativity through the generations. When Tarantulas discovers Megatron's plot, he jumps at the chance to potentially avert the destruction of his ancestral homeworld.

The Maximal and Predicon symbols are based on the leaders at the time of the great upgrade
They had to come from somewhere

Waspinator was responcible for the great upgrade
After the beast wars, Waspinator took The Slow Path back but still wound up on Cybertron before the great upgrade. After being studied for a while the data collected was used to create the great upgrade