I'm probably not the best person to start this thread as I've never read a comic (besides The Beano and Sonic the Comic) but I'll do it anyway. 
 
Obviously in this entire series, you have loads of Marvel characters going at it. If you strip away all the gameplay balance (as little as it was in MVC2) which character would come out on top? Within their own fiction, what would the Marvel tier list be?
  
I'm going to limit this discussion to characters that have or will be in the Capcom fighting series. 

I'm pretty sure Hulk would be God tier. I read that in the comics, he beat Onslaught who was by far the most difficult Marvel VS boss.

I am trying not to be a nerd. Hulk only destroys   Onslaught  armor.  
 
Buy yes. Hulk will be pretty high up there. 

Depends on which personality Hulk is bringing to the table, most of the time.  He's either nigh unstoppable or can be taken out in a matter of minutes.  Thanos with the Infinity Gauntlet has to win pretty much any contest, though.

shuma gorath is easily the most powerful marvel character in these games. its weird that they even include him.

i just want a Marvel Vs DC game, and see Superman punch a hole in Spiderman's face.

Magneto. 

Deadpool is God tier in terms of comedy...

I guess it makes sense to have Thor in the God tier?

Who would be the flat out worst? Who would be eventually matched?

" Who would be the flat out worst? Who would be eventually matched? "

I feel like such a nerd right now about to say this - given the line-up of current Marvel characters, without going and looking, it would be whichever mutant/character falls into the "Omega level mutant" category - which I think, for the MvC games, is Iceman.  Unfortunately, despite Iceman's unlimited amount of power, the fact that he doesn't comprehend the amount of power he could have means that he's not quite at the level of being able to perform as an omega level mutant, meaning that he may or may not be able to win - if he was accepting/aware of his potential, he would easily win, but if he's not, then he probably wouldn't make it quite that far.  
 
So, if given that Iceman isn't up to his fullest, I would say Deadpool.  Because he's amazing and you really can't kill him.  
 
Worst.. no idea.  I guess Sentinel.  I mean... those things get destroyed constantly in the Marvel universe.

" I guess it makes sense to have Thor in the God tier? "

Wolverine must be pretty high. He's nigh indestructible.

Phoenix, Iceman and Elixir I believe are all Omega level mutants making them effectively 'God tier'. Same with Magneto and Professor X maybe?

If Dan was in the game. It would be a no contest on who is on the god Tier.

The One Above All is of course the most powerful entity.