Personally I went with the underdog Apoc on this. His plans for domination are just as ambitious as Doom's or any other villain wanting to take over Earth, but he has the patience and life span to wait it out. He attempts something, and if he fails he goes into the shadows planning for the next attack. Plus doesn't Ozmandius (spell check? always get his name wrong lol), which is/was his right hand man seemed able to practically predict the future, which gives Apoc a good edge.
Like said his strength has been listed as incalcuable (meaning if he's drawing on an infinite power source he has a hulk like ability), couple that with his ability to change his size (as how ant man's changed size gives him strength proportional to his size), and he's incredibly strong. Toss in his durability, energy blasts, ability to change his body to other forms, and ability to practically create powers, and again he's a threat to most teams or hero's.
Couple all of that with a life span dating back to Egypt, figuring out how to use technology that was actually alien (and from a powerful group of aliens at that), and he's got the mind to match. He's seen more things happen than Doom, and probably knows more about the World's overall secrets. Plus it kind of seems his destiny to eventually win, even if it's long after the lifespan of todays hero's. He won in Cable's alternate timeline, and actually won in AoA which does count because it wasn't alternate, it did happen, but was set back to normal by a time traveling Bishop. Plus his ability to create flunkies is pretty good, he's had some powerful horsemen in the past, he altered Sinister and probably has taught a lot to him, and sinister's considered the expert in the MU on anything gene related. Though I'll admit he's had his down moments, he always comes back a bit stronger, plus count that his powers are so great he has to switch bodies because no container can hold his power for too long, and eventually he'll get his hands on an X-Man like body and he'll be even more powerful.
Doom's a close second to me, he always find a way to get near a win no matter the opponent, but his arrogance always keeps him from winning. His biggest and possibly only flaw tends to come out pretty often. Plus there's -