Oh… that’s a tough one.
There are a couple that I sort of have these weird, kind of irrational grudges against, and the biggest one of those is probably Rayquaza, which I dwelt on at some length last year.
I don’t have much of a problem with Rayquaza’s design, or powers, or really with any of the things normal people think about when deciding which Pokémon they like. When I think about legendary Pokémon, I normally think about how well they fit into the story and how they develop the atmosphere of the world, since that is, in my opinion, what they’re really ‘for’ – they are ‘legendary,’ after all. Rayquaza irritates me because his involvement in the climax of Emerald version is sheer deus ex machina and utterly robs the player of agency in the resolution of the Hoenn crisis. You don’t even get much satisfaction out of completing the Sky Pillar (which is much easier than on Ruby and Sapphire) or finding Rayquaza in the first place (since the scene with Wallace in which you figure it out is totally nonsensical). ‘Rayquaza fixes everything’ is simply not my idea of a well-done climax sequence.
Pokémaniacal 