I have an idea to end all ideas. This one will blow your mind. Take your next Pokémon game for the new WiiU and make it like my idea. In return, I want a copy and 0.05% of all the profits associated with the game.
For your next game, make it an actual training simulation of Pokémon. Like a virtual pet, but Pokémon, and better. Repeat an attack on this dummy to improve accuracy and speed. Run through simulations with other Pokémon. Have this Pokémon learn, actually learn how to fight. Then engage in online battles in a 3D environment with other people's Pokémon. It would be like the anime, but more engaging. "Fury Swipes has bad accuracy, so I trained my Pokémon to zig-zag to take advantage of it!" "RHYPERIOR, SANDSTORM AND DIG!" And all this would happen in real-time, combining your command speed with that of your Pokémon's speed. Instant reaction from a Whisicott and a two-second drag for the same move done by a Ferrothorn.
Limited trainer customization. What you have done so far is great. Stay with that. I don't wish to see rude and disturbing trainer's cards depicting phallic symbols.
Structured tournaments online using Smogon rules. I won't come back to a Hoenh region match if all I see are the Regi team rocking unsuspecting players.
Write a story using all the regions. Restart and use the region's Pokémon in all official battles, such as gym battles, the Elite Four, and any Pokémon-theme side game of the region. Sure, Team Plasma just got rocked by your Level 100 Charizard, but your Infurnape now has no EVs and is easy pickings for the Fighting gym. Trainers won't pay out unless it's a region-based Pokémon. You can think of something, I don't need to do all the work for you.
So again, I hope that you will take what I have typed into consider- OMG GEN SIX IS OUT MUST HAVE 3DS