In an interview with Game Informer, Pokemon Company director of consumer marketing J.C. Smith commented on why there isn’t a Wii U version of Pokemon X/Y.
Admittedly, the response is predictable. Smith mentioned that Game Freak tends to prefer portables as a result of the communication and trading aspects, and because you can take them with you.
“I can’t speak to the specifics, but traditionally Game Freak has always loved the game to be on a portable device because of the communication, trading, and the experience of taking this adventure with you. That’s why they’ve always prioritized a portable version of the game first. They’ve always liked what you can do in the real world with that.”
Speaking more broadly, Smith discussed the lack of real Pokemon titles on console:
“It comes down to what the creators want to do. Every time I’ve heard them talk about it, it’s been about the portable experience, taking the adventure with you, being able to share it with friends, communicate, trade, battle – really encouraging that interaction.”