Except to be 3 stage boss, you’d need Sentry. His first form is Sentry, then humanoid Void and then The godly Void from Siege.
Well at least the first stage sentry can just be a really cheap psychic AI sentry that deals a sH*t of a lot more damage than the actual playable Sentry 
A giant Seth Killian head that shoots authority beams, rainbow fireballs, and CAPCOM members. <3
Blackbolt is pretty ridiculous. I think he might be too powerful actually. lol He could destroy a galaxy just by speaking above a whisper. Cuz he is that awesome. Even though he is a good character in the comics and preserves order. I still think it would be amazing!
or Aunt May for the win! 
You know what would be a great crossover boss?
Vergil/Nelo Angelo with the Infinity Gauntlet.
Tyrant or Nemesis. Galactus would be extremely hard but its going to be another Apocalypse
Just put Seth as the final boss. That works fine for me.
And clutch bombs.
what even the final boss was something like cosmic Bison.
If i could fight any of the fallowing as bosses in MvC3 it would be either Carnage or Fin Fang Foom.
OR it would be M. Bison being taken over by the Symbiote.
Cyber Captain Hook 
Captain Planet…
I think Galactus would be a good final boss, but have Shin Aunt May (or Uncle Ben, for that matter) show up if certain conditions are met similar to Akuma in SFII.
i jus hope the boss is huge…like Ginormous…it would give more of a challenge…and not weak like the one in MVC 2…i think it should be a three part battle as well…
Lol dat would be crazy…
but Gill as Galactus’ new herald could be good, and add Sentry/Void with a T-virus even.
no recycled bosses please. galactus or sentry would be awesome.
it will be something halfe marvel half capcom (or 1 from each)
The big trick of the whole game is that the final boss is going to be Batman.
More seriously… uhh, Capcom’s side of things uhh… Vergil, Gill, Bison, or Wesker stand out to me as good potentials.
And on Marvel’s… Galactus, Doctor Doom, or even Loki might work.