Xatu. Poor, poor Xatu. The stiff gliding position it's in really doesn't look nice at all. Skarmory, Tropius, and Swellow also suffer from this. It just looks so awkward.
Xatu would definitely look better standing. Pretty much any rock type. They don't really look like stone, they're just too smooth and not craggy enough.
Surprised no one has mentioned Quilava and Typhlosion. As much as I love the Cyndaquil line... they just look bad. Like sausages. It's just really awkward. I also think Lopunny is kinda weird, because of how flat its ears are. Shouldn't they be more fluffy? And finally... M-Salamence. God bless M-Salamence. Why are his legs like that? Just hanging off to the sides? And his wings look like they were just glued to the top. I feel like it's just gonna fly off any second.
Honestly? All of them look pale, waaay too pale on both classic and MD. Come on, nintendo, you did better in 2006 with Pokémon revolution, add some color value for god's sake.
Yeah that's a good point, I've noticed that too. I mean look at Pikachu, their own mascot. They really need to up the saturation.