Wolverine's healing factor fluctuates a ton... But it is still only the normal human healing processes accelerated by an insane amount. So logically, he should't be able to regrow organs and such, but he does. Those are examples of Wolverine gone too far. He should not be growing full organs, simply because that's not how his healing works.
As to his offensive victories, his claws have also gotten sharper and sharper. He doesn't have the strength to cut Colossus or the Thing, yet he can stab Hulk nearly to death? Especially when Hulk heals many times faster than Wolverine does.
That said, he should take Snake down. Bullets are pretty much crap to Wolverine. A couple of slashes should do the job. But many people argue against Wolverine because he fluctuates a lot more than most other comic book characters. So the range and frequency of him doing things he should not is pretty big.