Crystal, just be glad this isn't FVII Vs FFIX
I dunno how to answer this. Cloud does seem pretty cool and is the one who defeated Sephiroth twice. I count all Naruto characters as undeniable Mary-Sues. I mean, they can do all these kick-ass Jutsus ... but SAKURA STILL SUCKS! She only ever seems to want to get into Sasuke's pants ...
Anywho, I must way up:
SOLDIER Vs Sensei
Genetic Enhancement (this did happen, didn't it? :\) Vs Sharingan
Magic/Limit Break Vs Justu
Buster Sword Vs Kunai ...
3D Vs 2D ...
Meh, I dunno who would win. I'm leaning towards Cloud though.