Two things have always bugged me about Zelda:
1. All the bosses (barring the occasional miniboss) follow the same formula: Dodge attacks, use item/technique you acquired in the dungeon to expose their weak point, wail on weak point with your sword, repeat two more times, win. Seriously, this has been the pattern for every boss of the Zelda games, from Aquamentus in the original LoZ to Ganondorf in Twilight Princess. Granted, the last boss of TP sort of broke up this formula by going for a straight-up sword duel (which was great fun, I'll admit), and that's a step in the right direction, but really, it isn't enough for me. I'd much rather have bosses that don't make their weaknesses blindingly obvious. And really, would a little variation kill them? Why can't I just huck bombs at the boss if that's how I want to do it? Maybe I prefer to use arrows, why is that not allowed? I say, if it hurts regular enemies, it should be fair game for bosses as well.
2. No jump button (except in Zelda II and some handheld titles): I'm aware that this is kind of nitpicky, and that unless the game was specifically built to accommodate it, a proper jump button would break most 3D Zelda games wide open, but it really has always bothered me that I couldn't just jump around like an idiot. I find jumping really fun in most games, it's as simple as that.