Honestly....this is hard to choose. Besides the CD-i titles, Zelda has never really had a "bad" game. I love all of the console titles to death. However, I am not big on the Oracles or Minish Cap, but that's probably because they were made by Capcom, so they were a bit different from Nintendo's style. Don't get me wrong though, they're still Zelda games and I still liked them. Minish Cap has got to be my least favorite though.
MC had a weird graphic style, to say the least. Generally, I don't like the style, it just doesn't feel like Zelda to me. Just every time I looked at them, I'd think: "This is one of the main Zelda titles?" Also, some of the quests were annoying, such as all of the stones you have to find. Some of the music in it I just find redundant, while some tracks I just love. Speaking of music, Royal Valley has got to be the freakiest music in all of the series. It gives me the shivers, I kid you not.
Lastly, Vaati was way too hard. Nintendo usually makes their final bosses a little difficult, but not too frustrating and flat-out unfair, and not too long either. With Vaati, you have to go through three rooms of tough enemies before reaching him. Then he has three phrases, and you have to do that all without dying, or else you start over.