Kalos Pokémon League is my vote for worst stage in the game. Sure, it looks nice, has cool music, and background Pokémon are a neat detail, but it fails completely when it comes to gameplay. Transformations are random and most of them are unbearable.
Water: it's okay. The stream only lasts for two seconds and lets you jump on the platforms. Manaphy's Whirlpool may be deadly, but it's not so difficult to not be stuck on it.
Dragon: geyser-like hazards are annoying. There's worse, but it's still annoying. Rayquaza... well, now we're starting to talk about this stage's most stupid hazards. He's fast and hits hard, and he's not super easy to dodge.
Fire: oh god those flame pillars, they're killing the fight. They inflict slight hitstun to fighters, which is annoying to move and land attacks. When Ho-Oh is here, the stage becomes downright unplayable.
Steel: if each chamber was its own stage then this one would be my most hated one by far. Swords as just as annoying as Fire chamber's flame pillars, and combined with the steel puddle that turn anyone touching it into metal, it makes killing anyone impossible. Also Registeel is one of the worst hazards ever seen in any Smash Bros. game. Stomp + swords swirl is almost impossible to dodge.
When I was working in the All-Star hard on everyone before I hammered this challenge (I couldn't resist the appeal after being KOed by G&W's Judge's 9 in the last round while I was working on WFT) I generally leaved immediately when this stage showed up. This is how much I hate this stage gameplay-wise.
Honorable mention to Pac-Land and Yoshi's Island. The former looks bad and has obnoxious hydrant hazards while the later has an horrible layout. I don't like Boxing Ring either, those ropes you can bounce on make it rather obnoxious to play on - b-but, it has cool character-specific aliases! This is negated by the fact that they also appear in the Omega version.