My biggest problem is that the game goes from okay during the first 3 temples, to "holy shit fuck awesome!" after you get the master sword, but then loses a lot of momentum when you reach Zant and Ganon. I know some of you could care less about the story in Zelda games, but a major reason why OoT's ending (to me) was so damn satisfying was that you met Ganon early on, and he kicked your ass easily, but you came back stronger than before and confronted him in an (imo, better directed) epic final battle. In TP, you were just some little tagalong that just happened to be there to Ganon.
And then there's the issue with the music. Fucking Nintendo, I swear. This has arguably the worst and most forgettable music in the Zelda series so far, imo. I literally cannot recall any really good tracks, aside from the Hyrule field theme and Princess Zelda's lullaby (which is just a remix of a theme done 15 years ago). And no doubt the ones that were good were most likely done by Kondo, just like in WW. Nintendo should fire the other two losers who worked on the music (one of them being the same chick who did the score for NSMB). Seriously, you'd think Nintendo would at least use some of their more talented composers, like from the FE team or something. And this isn't even including the sound quality which is just pathetic.