I prefer Ganon (Or Ganondorf) as the main baddie. Though I didn't like him in TP (To be honest, that whole plot messed me up. Still not sure I get it. Did Ganon really die, because the game said Zant wouldn't die unless Ganon did. But isn't Ganon immortal?) While I didn't like him in TP, I did enjoy him in WW. Something about seeing a more ... I don't want to say real, but less cliche that other versions of the character. He wasn't the typical all-evil Ganon. They showed him as someone who was envious, jealous of what Hyrule had (Not someone who wanted power for power's sake). And the ending with the sword in his head and him laughing quietly. I dunno, just does it for me.
So yeah, I'd like to see Ganon again. But it's time for Nintendo to step up what this guy can do. Zelda has become far too flat, and I hate to even feel that way. The series can never stray far from it's core, of dungeons and figuring out puzzles. But what it can do, is change boss battles. And try to really make newly acquired weapons useful throughout the entire game. There are far too many items that are only needed in a handful of places, then you don't even need them anymore. I would also like to see more alternatives to how an enemy is beaten. Not always with the item you acquired in that dungeon. And last but not least, it's time to ditch the 'memorize the big bosses moves, counter attack and repeat two more times.' Let's get some epic battles going on here.