Well, WW annoyed me in two ways: The poor design of the overworld (A FUCKIN' BOAT? THAT TAKES LIKE, HALF AN HOUR TO GO ANYWHERE?) and the obviously missing dungeons. Nevertheless, the game was good.
TP annoys me in one, big way: Missed potential. I mean, this game could've been so much BETTER. More caves, more secret dungeons, more ways and places of using the items (For example, LOVED the idea of the spinner. In practise, it's useless because it doesn't do enough damage and slows down way too fast, and there's about three places where you can use it). More sidequests, more people to talk to, do things for. More minigames.
This is gonna sound bad, but I really think Nintendo could've afforded to take another couple of months and put... well... more into the game.