Hmm. Interesting. Too bad my main interests (Doc Doom, Magneto) are already taken. Let's see. I'd be interested in starting with one character at most and there are a couple I'm potentially interested in. I figure I might as well just list them and see if any of those are particularly wanted and/or needed:
Dracula: The Lord of Vampires has a standing grudge against Apocalypse (if we consider the crossover comic featuring Apocalypse and Dracula canon) and has plenty of reasons to oppose him. Vampires do not evolve as the living do, but mutant blood is quite potent -- with a cadre of vampiric superhumans under his control, the mutant apocalypse might well turn into a vampiric nightmare. Luckily, Dracula realizes that too many vampires are a severe drain on his food supply and is quite a bit more sane than En Sabah Nur, so his might be the lesser evil.
Namor the Sub-Mariner: The Avenging Son already helped get rid of the last menace that declared itself the superior race. With pollution increasing and more and more aquatic mutants appearing, even the oceans are no haven from Apocalypse. Also, the on-again-off again villain BFF need to be reunited.
Mr. Sinister: The master scientist who shares much with his creator, Apocalypse, but certainly not his singular vision for the world. AoA-esque, I'd imagine him to have gone traitor after having been part of Apocalypse's leading cabinet.
Sebastian Shaw: What's the Black King of the Hellfire Club to do in a world in which luxuries and corruption aren't nearly the source of power they used to be? Why, build some Sentinels for the humans, of course! Definitely not influenced by the movie version, thank you.
King Hyperion: Interdimensionally stranded. Similar to Doom, the madman wants to take over for himself -- may be too powerful, however, considering he is basically an evil, even stronger version of the regular Hyperion.
Citizen V/Baron Zemo Jr.: Humanity must survive -- though hungry for greater power, submitting to the Apocalypse is not on the agenda. With many connections to various villains all over the world, perhaps it is time for the new Masters of Evil to wrestle power from the mutant overlord.
Venom/Eddie Brock: In an apocalyptic world, even the greatest of grudges take a backseat. The Lethal Protector does what is needed, this new world seems even better suited for his brand of justice than the old.
Ghost Rider/Daniel Ketch: Penance Stare may be a wee bit too potent in this uncompromising setting, but the Spirit of Vengeance has much, much to do and little time.