My least favorite stages, in order of most suck to least.
1. Mushroomy Kingdom- Oh my god this stage is so annoying! The side-scrolling battle thing just doesnt work for me. The characters aren't made to move that way.
2.New Pork City- I think everyone pretty much agrees with this one.
3. Spear Pillar- Most broken stage in the entire game.
4. 75m- It's so hard to attack anyone because there are basically no platforms of a decent size. It's just too busy and crowded.
5. Pictochat- It just becomes so annoying. Some of the drawings are just cheap beyond belief, and if you get caught on the wrong side, you're no more than a target.
6. Lylat Cruise- It just feels too small. There's no room to move.
7. Hanenbow- It's a cool concept, but it's the only stage in the game where the water buoy you for a while at least. It's really rather annoying.
OH! And one more. Shadow Moses Island when playing DeDeDe. He can chain grab you literally forever.