Hm, this is a tough topic...
If I absolute had to lean against one or two, I'd say Pokémon Black 2 and White 2. While they are special in their own, unique way, them being sequels didn't quite work in my eyes (and many other people, am sure). Somehow, it seemed as if they hadn't put much thought and tended to rush, causing its plot to seem like some rehash of sorts rather than an entirely different game.
I do understand that Black 2 and White 2 are meant to be connected to its prequels--Black and White, which, in my opinion, were actually marvelous--but I don't necessarily believe it was a good idea for them to make them this close. Had they been a little more far, I'm sure it would have been a lot better in general. If they create any other main-series Pokémon sequel at some point in future, I hope they take this into consideration, if they're able.