Villain Pedigree

Dean Winchester: Well then, good luck stopping the Apocalypse.
Sam Winchester: Thanks. Good luck killing Death. [beat] Remember when we used to hunt wendigos and stuff?

—The main characters of Supernatural reflect on this trope before going off to their penultimate showdowns of destiny.

A sub-trope of the Sorting Algorithm of Evil. That trope is about when individual villains become So Last Season as the heroes start facing new, more powerful enemies. This trope is about when this happens to an entire breed of villains.

For example, suppose there's a TV series called Spirit Hunters where a team of paranormal investigators travel around the country fighting malicious ghosts. This lasts them for two or three seasons, but after a while the ghosts start to get a little dull and repetitive, so the writers decide to shock the audience and have what looked like an ordinary haunting turn out to be a demonic possession. The demon adversary is more vicious, more dangerous, and has lots of cool Hellfire special effects surrounding it. The audience loves it.

So, as the series goes into season four, the Spirit Hunters start facing more and more demons, maybe even fighting against a demon Big Bad. It eventually gets to a point where there are only a couple episodes each season dealing with ghosts; the rest of the time it's demons, demons, demons.

Congratulations ghosts, you've just been replaced by bad guys with a higher Villain Pedigree.

See So Last Season; compare the out-of-universe equivalent The Taming of the Grue.

Examples of Villain Pedigree include:

Anime and Manga

Particularly obvious in JoJo's Bizarre Adventure, since the nature of the Big Bads changes with each part of the story. In Part 1, "Phantom Blood," the Big Bad is vampire Dio Brando, who's created an army of zombie Mooks. In Part 2, "Battle Tendency," vampires have been relegated to Mook status, while the Pillar Men (the creators of vampires, and far more powerful) take on the role of main antagonists. In Part 3, "Stardust Crusaders," Dio (still a vampire) returns as the Big Bad, but almost all of his vampire abilities are ignored in favor of a new fighting system based on "Stands," and almost all of his underlings are humans who also possess the Stand ability. And from Part 4 onward, vampires and all related beings are completely absent, with human Stand users being the only villains.
At the start of Dragon Ball, pretty much all villains were either wild animals or human beings (well, human beings and whatever the hell Pilaf was). However, starting with the Demon King Piccolo arc, there were pretty much no human characters left who could give Goku a challenge, so Akira Toriyama made all future Big Bads demons, aliens, androids, or something equally inhuman. Almost any conflict between Goku and a human martial artist after that point is a downright humiliating Curb Stomp Battle.
Happened to Bleach in a big way. The whole premise of the series, originally, was Ichigo using his shinigami powers to fight Hollows, ghosts who had been twisted into monsters by their own hunger. However, after Ichigo defeated hundreds of Hollows in a single day, including one the size of Godzilla, they were retired as villains for a long while, and other shinigami (many of whom could mow down the Godzilla-sized Hollows with ease) become the primary villains. Hollows do return later as a force to be reckoned with, but only by gaining Shinigami powers of their own and crossing the Bishonen Line.
Likewise, in Busou Renkin, the original monsters were human-eating monstrous homunculi. Eventually it got to the point where our heroes could beat a whole hoarde of them and still have enough energy to face the Big Bad and hold their own. It was at that point that no new homunculi characters were introduced, and the villains became humans with Busou Renkin themselves, and way more fighting experience.
The Magical Girl type Monsters of the Week in Lyrical Nanoha were quickly regulated to easily-dealt-with distraction status by the half-way point of the first season as the series moved to battles against other mages and knights, armies of Anti-Magic protected Mecha-Mooks, and different kinds of Super Soldiers. When one such monster showed up in first Nanoha Striker S Sound Stage, it was treated as something for the rookies to practice what they learned in training on.
My-HiME starts with natural Orphans as the basic monsters, then progresses to Searrs-made Orphans, then Searrs troopers proper, before culminating with each other.

Comics

Superman, as well as most other superheroes created during The Golden Age of Comic Books, started off their careers fighting ordinary human criminals, Nazi soldiers or even just factory owners who didn't treat their employees right. Having a superhero fight an equally powerful supervillain was originally a rare, though very exciting, event. It wasn't until the Silver Age that superhero/supervillain conflicts became the staple of superhero comics.
Some of the Silver Age villains that Daredevil fought have been forgotten or turned into a Harmless Villain when Daredevil became Darker and Edgier in the 80s, especially when Bullseye and Kingpin became Daredevil's Arch Nemesis. Some villains like Mr. Fear and Purple Man have been updated to fit this new Dark Age, but others, especially Stilt-Man have been left behind.

Live Action TV

Stargate SG-1 First there's the Goa'uld, who have their own Sorting Algorithm of Evil. But rapidly they loose place to more formidable villains like The Replicators or The Ori, by the end of the show the Goa'uld are almost finished and a Goa'uld plot is more seen like a minor break from bigger story arcs involving meaner villains.
Buffy the Vampire Slayer was supposed to be about a girl named Buffy who fought ... well, vampires. She was never limited to just vampires, but, for the first couple seasons, vampires were the Big Bads and represented a serious threat to Buffy. The third season changed this by having a non-vampire Big Bad who used vampires as minions. By the fourth season, the series could have been accurately renamed Buffy the Demon Slayer, with vampires simply one of many demon species (and pretty low on the demonic totem pole at that). During the last three seasons, there were usually only a couple vampire-centric episodes each year; the rest of the time these formerly main villains were used as punching bags whom the good guys could kill off when nothing important was going on. The last season made a nod towards the title by having the villain command a legion of, essentially, super-vampires. After the first one they were still pretty easy to kill.
Smallville, for a long, long while, kept its villains limited to two simple categories: normal human beings (usually with access to Green Rocks), and people who were granted superhuman abilities by those Green Rocks. It wasn't until the fourth season that a few villains started turning up with non-kryptonite based abilities. This jumped up a notch in season five, when Brainiac (an alien-built robot) was made the Big Bad and a few evil Kryptonians showed up to hassle Clark. The number of alien adversaries has only increased from there, with meteor freaks, once the staple villains on the show, reduced to a handful of appearances. However, since the alien baddies are usually able to go toe-to-toe with Clark physically, rather than getting taken down with one punch, most fans haven't complained.
- Particularly as the sheer number of people in this small town who gained superpowers was making it implausible that people wouldn't learn Clark Kent was from Smallville and immediately think: I wonder if he has superpowers.
Charmed changed its Villain Pedigree fast. When the series started, while many different kinds of supernatural villains would turn up, the principle baddies the Charmed Ones were supposed to face were warlocks, evil witches who steal the powers of good witches. However, by the end of the very first season the main warlock antagonists had been killed off, and a pair of demons ended up taking center stage during the season finale. Warlocks would still appear after this, but far less frequently as time went by, while demons would appear more and more often. By the end they made up something like 90% of all bad guys on the show.
- Warlocks were heavily featured for the first three seasons of Charmed but by the end of the 8 seasons, warlocks hadn't shown up since two seasons before.
Demons seem to do this a lot, don't they? The example in the trope definition is a spot-on description of Supernatural.
- To go into more detail: when the series began, Demonic Possession was a pretty big deal, and just one demon caused them considerable grief. By season 4, demons still cause them grief, but only the leaders. The bog-standard "black-eyes" are hardly the threat they were before. Ghosts, moreso.
  - And in season 5 demons have had this happen to them with Angels having a higher Pedigree. The new Big Bad is a Fallen Angel (rather, THE Fallen Angel) and there's all those other angels trying to bring about the end of days.
- There's also the manner in which demons are disposed of. In the early seasons, the brothers have to do lengthy exorcisms to get rid of one, and that only sends it back to Hell for a time, free to come back anytime. The McGuffin in the first season is a special, unique gun that can kill a demon permanently. The catch is that the gun has only 6 bullets - the brothers can't afford to miss. It's the only thing in the world that can kill a demon. They tell us so. Repeatedly. That is, until they're given a knife that does just that, whenever they want. And shortly thereafter the gun gets modified to fire as many bullets as they like. It gets even worse when Sam learns how to exorcise or even kill a demon with his mind. Demons were retired for Lucifer after Sam killed the first and presumably one of if not the most powerful demons, by pointing at her. Yeah, they kind of had to switch up at that point.
- Lampshaded when, in the season 4 episode In The Beginning, Dean goes back in time and is called crazy for suggesting they try to kill a demon. By season 4, Dean and Sam had already racked up a considerable demon body count.
- And season 7 goes yet another step further, retiring angels to replace them with Leviathans. So, to sum it up - to this point, at least - the pedigree goes: Ghosts < Demons < Angels < Leviathans.
- Though the leviathans could be considered an aversion of this trope, as their main abilities seem to be limited to shapeshifting and Nigh Invulnerability, and they have a Weaksauce Weakness in the form of borax. They're almost certainly weaker than the also nigh invulnerable face-melting reality-warping time traveling dead-resurrecting angels and, if it weren't for the aforementioned knife, would probably be rivaled by demons. If the angels weren't busy dealing with the aftermath of their civil war, they'd probably still be running the show on Earth.
Arguably Doctor Who. When it began, many of the stories centered around the TARDIS crew landing in an otherwise ordinary Earth setting and lacked any real Sci-Fi elements beyond the TARDIS crew; for example, the first serial dealt with one member of a tribe of cavemen trying to usurp power from another. After the first couple of Doctors, however, such human villains were largely displaced, and every storyline was obligated to feature some sort of alien presence or something, though human Corrupt Corporate Executives, Mad Scientists, President Evils and General Rippers continued to pop up and still do.

Literature

When Timothy Zahn kicked off the Star Wars Expanded Universe, his bad guys were Imperials trying to recover the territory lost to the Rebellion/New Republic after the Emperor died. Almost the entire Bantam era has, as its villains, the remains of the Empire, as well as occasional offshoots. A few times strange aliens were fought instead, and nearly every author felt they had to spring a Superweapon Surprise, but it was nearly always New Republic versus Empire. In the Hand of Thrawn duology which capped the Bantam era, the battered but proud Imperial Remnant signs a peace treaty with the New Republic. Stories set before that point may still have Imperial villains; stories set past that point may have offshoot Imperials, but these days there are fewer books with either. Now strange new aliens are the go-to bad guys, from extragalactic sadistic masochists to hiveminded bugs controlled by evil burn victims to, most lately, Cthulu. Again, there are exceptions like all Clone Wars and earlier books, and one series had a civil war, but strange new Scary Dogmatic Aliens seem to be the current menace.
- And Sith- mustn't forget the Sith. They really started out as extra special, extra dangerous villains, but now they're everywhere- Legacy and Legacy of the Force had Sith Big Bads, while Knights of the Old Republic and Fate of the Jedi have Sith among their villains in various ways (not to mention anything set during the clone wars or the Galactic Civil War will have Sidious/the Emperor as Big Bad by default). Of course, the Sith are certainly Scary and Dogmatic, even if they aren't all aliens, so they could also be said to fit in with the above as well...

Tabletop Games

In Dungeons & Dragons, humanoid enemies like goblins, orcs, and kobolds only remain challenging for the first few levels (unless they have class levels).

Video Games

This is a common trope in video games in general. The new areas that the player goes through usually bring with them new types of enemies that may gradually replace the ones of previous areas.
In the mediocre Warhammer 40,000 FPS Warhammer 40,000: Fire Warrior, you start out fighting Imperial Guardsmen. After some point you start going up against Space Marines. Later still, with an Enemy Mine in place, you move on to Chaos Space Marines and other servants of Chaos. You won't be fighting any more Guardsmen by then.
Similarly in the strategy game Rites of War. Your Eldar will first fight some Imperial units, but eventually they'll ally with you to fight a Tyranid invasion.
In the Ratchet and Clank game "Tools Of Destruction", the player starts by fighting the villain's simple mercenary armies. However, in the second half of the game the mercenaries are replaced by monstrous Elite Mooks from the villain's own race who can phase in and out of matter.
In Castlevania: Symphony of the Night when the player gets to the inverted castle and is vastly more powerful, many of the regular mobs are actually the bosses from the first castle.

Web Comics

While Order of the Stick has kept the same Big Bad and Dragon for its entire run (so far), the level of enemy Mooks has gotten raised, with Xykon replacing all of his goblin soldiers with the stronger, more militant hobgoblins.
- Justified by the fact that between the Order itself and the Dungeon of Dorukan exploding, Xykon probably lost most, if not all, of his goblin army.
- Also justified in terms of plot mechanics—since the heroes are gaining XP and getting stronger every time they fight, the mooks they're pitted against have to get tougher too, or the whole balance of the world will be thrown off.