I voted Vaati and Ganondorf, but I would much rather see Vaati. Ganondorf is very unlikely at this point, but I think Nintendo can still come up with a way to put him in SS if they wanted to, like time travel. Besides, Ganondorf has been in all of the major Zelda games, so I can't really imagine him not being in SS in some form. It just wouldn't feel right, IMO. I never get tired of Ganondorf anyway. No one ever complains about Bowser appearing too often in Mario (to my knowledge), so I don't see a problem with Ganondorf.
I wouldn't mind a new villain as long as they put effort into him/her. I don't want them to pull another Bellum or Malladus. And I really don't want Dark Link to be the main antagonist. That just seems like it would be another lazy move by Nintendo, because he doesn't talk, and there's not really much you can do with his character. Besides, the whole "dark version of the hero" thing is just so cliche. I would rather him keep his role as a magical conjuration. Giving personality to Dark Link just doesn't feel right... It sounds like bad fanfic to me.