I'm gonna go ahead and be the one that sais this discussion is absolutely absurd.
First off, because most of these mutants/beings have very, if not most similar powers.
I'll go ahead and throw in my realistic opinion though.
'Cosmic'
Beyonder, preferrably because he can manipulate anything.
Thanos, preferrably because of the manipulation as well as the mind control.
Galactus, preferrably also because of manipulation as well as denying physics and controlling galactic forces.
'Non-Cosmic'
Mr. Sinister, let's see: Superhuman everything, shape-shifting, fast healing, telepathy, telekinesis, immortality, did i miss anything?
Apocolypse, Superhuman everything, invulnerable, manipulating, rearranging things, teleportation, telepathy, telekinesis, immortality, mind transferral.
Toad - Because i had to give an absurd answer, you know.. like spider-man, batman, sabretooth, wolverine, etc.
On a side note, those of you that mentioned things like "oh spider-man defeated thanos, and they took him away in cuffs" or whatever, let's all just remember one thing, its a damn comic book, the good guy wins 90% of the time. Think more realistically, ok? thanks.