Pokémon X/Y is probably the most innovative Pokémon game that pushes the limits of the 3DS with it's graphics that look like Half Life (GoldSrc Engine), but can render bigger environments.
But, the game is seriously harder than it looks. There is too much NPCs, some Pokémon are strong (e.g. Hawlucha), gets you frustrated after playing a bit.
This game IS innovative, but also trolls you in many ways.