I thought this might have been a victory for Wesker too, but I can recall some nasty feats from Chun Li in the SF anime. Like this one...
[youtube]T51U8uQFrQo[/youtube]
0:50-0:57 she decimates Bison with a large energy blast strong enough to leave a large crater in the ground. One that looks to be several meters deep and at 1:18 and 1:44 looks to be at least a kilometer across if not more.
Wesker is tough, but I would question whether or not he could survive a blast that intense head on. Chun Li took the full force of that blast head on, so I would also question whether or not Wesker would have enough power to put her down. Especially when Chun Li took Bison's even larger blast right after and didn't look injured.
From what I recall Wesker doesn't have that kind of raw power. His speed should be comparable to Chun Li's, if not greater, since he can dodge sniper rifle fire at point blank range and snatch rockets out of the air. Wesker is tough enough to survive being thrown into lava but that's nothing compared to Chun Li's Kikosho, which obliterated all the vegetation, rocks, and trees around her leaving a smoldering crater behind.
So this is where I'm at: clearly Chun Li has the power to kill Wesker, even with his regeneration. He's never survived an attack powerful enough to leave a kilometer sized crater into the ground. But is Chun Li fast enough to actually hit Wesker? The drawback is that she has to be right next to an opponent for the Kikosho to have a full affect.
Perhaps she could try and hit him with a weaker version of the attack to try and damage him enough to finish him with a full powered attack, but I don't see that happening. Without that attack Chun-Li should be somewhat comparable to Juri, who kicked jet fighters in half with her raw strength, so she could feasibly damage Wesker with her kicks until he's worn down enough. But again, Wesker's speed and regeneration would make this difficult. Otherwise I see this battle being a stalemate.
Wesker doesn't really seem to have anything that could feasibly put Chun Li away and I'm not sure if Chun Li could contend with Wesker's speed and regeneration combo.
If I had to chose someone, I'd chose Chun Li, because she does have a clear way to win if she can connect with her full powered finisher.