Forgot about Skyward Sword. Dang it. Well, then I'll definitely that predict Link/Ganondorf wins, then.
It's almost as if fate aligned that game's release date with this contest!
Edit: the logic of Cloud/Sephiroth winning is, in addition to their overall strength as individuals being stronger, Cloud/Sephiroth could be argued to be more popular as an actual rivalry itself. There's the final battle scene between them, some major spoils involving them that I won't say, and they have been in lots of polls ("which do you like better, Cloud or Sephiroth?") for years. They are both -very- iconic RPG characters.
Link/Ganondorf isn't bad, but it pales in comparison to, say, Mario/Bowser. Even with SS, I wouldn't be surprised to see it lose... except I'm still expecting it to win with ease, with this site being Zelda-FAQs.
--
"Ah, a party! We haven't had one of those. So...what is a party?"
"Well, you drink punch and eat CAKE! ...I think."