My least favorite game is Wind Waker.
I just want to clarify two things. First, this is only considering the games I've actually played. If I were to have played Phantom Hourglass, I suspect I would be putting that here instead of WW. Second, you have to realize how highly I think of the Zelda series. Saying it's my least favorite isn't really saying much for me.
My reasons for liking WW the least? Well... first off it follows the trend of the modern Zelda games, and that includes being too easy, dropping more classic elements, etc.. I thought it was the easiest Zelda game, and that bugged me. Second, I thought the boat was a good idea, but I don't believe it was executed that well. There was very little time spent on land. Land gameplay has always been part of the Zelda series, and I thought that with the exception of dungeons, WW largely phased this out. If they were going to make a game with so much sailing, then I think they should have polished it more so that it was funner, had more to do, etc.. Really, the improper execution of the sailing is my key issue with WW.