Pokemon Stadium, with an expanded rental feature that allows you to pick the moves, items, nature and IV/EV spread of the Pokemon you rent. Obviously you can use pokemon from your game too. The catch is that you are stuck with the level up moveset for rentals...at the start.
Battling and winning in solo or in online multiplayer (local would be too easy to abuse) earns you BP that you use to buy TMs and Items for your rentals, which gives you something to work for. You can also unlock new Move Tutors to teach your rentals and your in-game XY pokes things like Hyper Voice. Egg moves you get on your rentals through a special egg move tutor. These are single purchase, unlimited use. If you competitive breed in game this shouldn't even be a problem. Otherwise you should practice in single player. What would that be comprised of?
Stadium battles akin to the Cups in the N64 games, in many styles (ie Ubers allowed, Little Cup, and Frontier style gimmicks) and formats (double, triple, rotation, sky, inverse(?), a horde mode (?), double rotation (?)). Gym Leader Castle now turned into an expanded World Tournament where you can battle all past gym leaders, elite 4, and champions, with vastly improved teams. A Stadium 2 type trainer school with puzzle battles (ie. Given a Venusaur and a Charizard with these moves/items, beat the Dialga and Palkia before you in 2 turns). And a Minigame zone.
I love Pokemon, but the Stadium games never did it for me. I found them to be boring and slow. Even if they made a full-blown Pokemon game on consoles, I probably wouldn't buy a WiiU for it. The Wii just didn't have the third party support I was hoping. Nintendo promised better third Party support with the WiiU, but they haven't delivered. Nintendo first party games are amazing, but sometimes I want to play something other than Mario/Zelda/Metroid.
A better idea would be a Pokemon university/academy game where you are a new student who has to go thru written and battle exams to rank up in the academy to unlock areas around the campus to catch different pokemon.
The goal would be to be the top student in the academy which would only be achieved if you managed to beat all the top battlers in the school who are the presidents of certain clubs like the swim captain and team only use waters types and to get to the top battlers you have to join their clubs/teams and only use that particular type of Pokemon. You would also be able to battle the faculty to unlock items,Pokemon,and discounts to certain shops around the shop.
You would be able to trade Pokemon with others who have the game and breed using the daycare on the campus which will tell you exactly how long it would take for an egg to pop up from the Pokemon you placed in there. Also events will pop up at different times on different days either around the school or in the Pokemon areas that will let you get special battle items or Pokemon that might not appear yet in the game.