ZeroMachine said:
One of the fundamental laws of physics is that Goku always wins, no matter who is fighting who.
So, Goku.
EDIT: Ohshit, gotta be honest, I didn't read the OP

you have that law covered. Sorry, dude.
Oh hey, you've gone active again.
On topic: No one really. Even if Alex couldn't win, he wouldn't lose either. There isn't a single biological thing he can't assimilate, and if you evolve his powers to their logical extreme, he'll sooner or later be able to assimilate inorganic matter as well. Shit, the guy can shapeshift on the molecular fucking level, according to whatever he wills himself to be. So yeah, maybe he couldn't kill Wolverine or Superman or whatever, but he wouldn't have to. He'd just infect them and eventually his genetic structure and consciousness would subsume theirs.
So that's how he'd win, but here's how he can't lose:
If he can shapeshift to such a degree, then it follows that he could craft a second Alex Mercer if he so chose. It would be a simple matter of copying and building a replica of his own brain and then separating a lump of his own biomass for it to inhabit. QED: If you killed an Alex Mercer, and totally fucking erased all traces of the body, there's still another one out there. And presumably he could just duplicate himself all day.
And all this is before we even consider that Alex Mercer is a high functioning sociopath with no real understanding or care for moral philosophy.
Re-cap: Alex Mercer has the mental capacity to exist and manipulate matter on the nanoscopic scale, the physical capacity to self-clone ad infinitum, but lacks the emotional capacity for his clones to develop individually outside of a hive mind.
Mercer is the fucking Omega Singularity. The end and the summation of all things.