Here's why Samus will win:

1) Samus has greater mobility. Cloud can fly, yes, but it has already been established that he can only fly for limited amounts of time before he has to rest, which leaves him vulnerable. In an earlier battle, I argued that Cloud could potentially sustain flight longer than he could in Kingdom Hearts, so long as he wasn't going "berserker rage" in the process, but either way, he's got a limit. Samus has greater mobility because she can remain airborne for an unlimited amount of time, and (by using the Screw Attack) during that time she is invulnerable to nearly all attacks.

2) Samus has an unlimited supply of ammunition for nearly all of her attacks. She has a Missile limit, a Super Missile limit and a Power Bomb limit. Aside from those three weapons, she never has to worry about draining her reserves.

3) She has a more versatile array of attacks than Cloud does. She has beam types that are energy-based, electricity-based, ice-based, and fire-based. She has a large number of enhanced attacks and special abilities that make her into a one-woman army.

She's got all of her bases covered. She might not do as much pound for pound damage as Cloud does, but she's much more versatile and is much more easily capable of whittling down his health than he is of actually harming her.