Actually, Snakes main advantage over Bowser would be his immense long range capabilities. He may take long to set up, but running with Bowser leaves (im not sure of the exact figures) a moment of frailty, a "blind spot" if you will on Bowser. He is very easy to intercept, especially with Snake. Snake has the awesome ranged game going, and he can gimp on Bowser quite easy with Grenades and his many other projectiles. And the fact of Bowser's weight doesnt help much either. He is too slow to effectively be much of a threat to Snake. Only threat I can see is the n00b kill Koopa Klaw suicide move.