Replacement Mooks

So, the Big Bad was defeated, his forces routed, and The Hero has saved the day. Sure, the villain escaped, for now, but everyone's going to be ready when he returns as promised. Besides, you've handled the worst he could throw at you. What could he possibly do to surprise you now?

But then, when the expected return happens, the heroes find an unwelcome surprise: our Dangerously Genre Savvy villain may have been defeated last time, but he ain't stupid. It seems that all of the weak, pathetic mooks the hero(es) barged right through last time have been replaced. Possibly, by something much worse.

Our Big Bad has brought in the Replacement Mooks.

This typically happens in series which retain a recurring villain. Said villain, after failing in his plans the last time, has seen fit to replace his forces with newer enemies for the hero, whether in part or in whole. This is usually because the villain is attempting to learn from his or her mistakes during the previous altercation—after all, if something doesn't work once, why try it again? New enemies could catch the heroes off-guard, or make it much more difficult to adjust. Or, the villain might just want to send a message about what happens when his minions aren't up to task.

Comic Book

 * Done as one of Robotnik's schemes in Sonic the Comic, where he basically exploits Sonic taking the games' difficulty curve for granted by transposing some of his more advanced badniks from a Sonic CD level into the Green Hill Zone.

Film

 * The Matrix Reloaded. After the failure of the Smith-model Agents in The Matrix, the Machines come out with improved Agents (which Neo calls "upgrades" when he first meets them).
 * The Incredibles centers around this trope, as the villain tests his robots against superheroes in order to improve them.
 * Every Terminator starts as this. The first one introduced, the T-800, was a replacement for the T-600. In the next film, the T-1000 replaced the T-800. Then, the T-X replaced the T-1000. Justified, because they're machines and SkyNet is just upgrading.
 * In the Star Wars prequels, the Trade Federation replaces its rather laughable battle droids from the first film with more advanced Super Battle Droids with a more menacing, dehumanised silhouette. One of them can be seen literally knocking the earlier models aside to get at the Jedi enemy in Attack of the Clones.

Literature

 * A realistic version of this shows up in A Song of Ice and Fire. When civil war wracks the Kingdom of Westeros during a Succession Crisis, the Kingsguard (bodyguards for the royal family) suffer several losses. When Jaime Lannister finally makes it back to the capital to take command, he's horrified and infuriated to find that he has two dependable knights left in the Kingsguard, while most of the other new members are political appointments, second raters, or amoral mercenaries.

Live Action TV

 * In Power Rangers, every new villain brings his/her own legion of mooks with them. Putties, Z-Putties, Tengas, Cogs, etc. This doesn't apply as much post-Space, as each year is now an entirely different story set in the same world, but some villains will introduce elite versions of their own grunts, eg Kelzacks becoming Kelzack Furies.

Video Games

 * In the Mass Effect series, the villainous use the robotic geth as their primary mooks in the first game. While they're still active in the sequel, their role as the primary mooks are taken up by.
 * In the third game, the new primary mooks are Husks, reanimated corpses of various species jammed full of cybernetics. They were around in the previous games as simple cannon fodder, but they now come in a variety of forms with various abilities. For example, Marauders (turian husks) can use guns and infantry tactics, Banshees (asari husks) can fly, throw out biotic attacks, and put barriers around allies, and Ravagers (rachni husks) have cannons built into their backs. However, the have also managed to strengthen their geth forces, and have successfully indoctrinated  even as it tries to do the same to them.
 * In the Halo franchise, the Prophets of the Covenant quickly replace the Elite with the Brutes after the former fail in the first game
 * When you beat Super Mario Bros. once and start a new game immediately afterward, all Goombas are replaced by Buzzy Beetles.
 * It happens frequently on Metroidvania style games, most likely after defeating an important boss, unlocking a new zone or obtaining a power-up.
 * In Paper Mario: The Thousand-Year Door, eventually the goombas and other basic enemies in the Rogueport Sewers are replaced by more threatening Koopatrols, Hammer Bros., and Magikoopas.

Web Comics

 * In Order of the Stick, Big Bad Xykon gets his goblin forces routed by the heroes during the first arc. Soon after, he finds an army of hobgoblins which numbers in the tens of thousands.

Western Animation

 * In Teen Titans season 3, Brother Blood's human mooks prove ineffective against the heroes, so he replaces them for the season finale with mecha mooks adapted from Cyborg's technology- which prove to be some of the toughest mooks in the whole show.
 * It seems like every season of the '80s-'90s Teenage Mutant Ninja Turtles cartoon has an episode like this, with Shredder and Krang replacing Bebop and Rocksteady, only for the replacements to be de-mutated, destroyed, or do a Heel Face Turn, forcing the baddies to re-employ Bebop and Rocksteady.
 * Eventually Shredder and Krang themselves were replaced by Dregg. For his first season on the show, he used Insect like creatures called the Techno Gang. Next season he used a race of batlike creatures as his mooks.