Well, with the shocking announcement of Pokemon x Nobunga's Ambition, what other video-game series would you like to see Pokemon crossover with?
The most obvious one in my mind is Koei's other historical series, Dynasty Warriors, a hack-and-slash which already has cross-overed with two popular series, Gundam and One Piece. Although, in that case, it was more like Mysterious Dungeon in that they took the system, but none of the characters, so the Gundams aren't beating up Chinese warriors or anything.
Dragon Quest x Pokemon would also be interesting, since I think the Dragon Quest monsters would mash pretty well with the Pokemon. Maybe a new Rocket Slime-esque game?
Persona x Pokemon. Hire the art director of Shin Megami Tensei to draw all the Pokemon in the Persona-style, that'd be amazing. You could increase your affinity for certain Pokemon types by forming social links with trainers.
Street Fighter x Pokemon. Enough said.