Idea for a game: "Pokémon Ultimate"
A game for home consoles encompassing all known regions and locations whether they be from previous games or the animé, taking place in its own time(re: not during other games). Having so much space to roam around, people to talk to, and tasks to accomplish is on par with an MMORPG in terms of concept art, programming, and writing so why not make it one? Starting areas are taken care of. A class system can be thought up quite easily depending on what direction you take it. Zones for higher level players already exists in current games as does the level-up mechanic and balancing. Super-rares and legendaries would be a concern of mine so making them legitimately hard to get instead of the default reward for completing the main quest is a must, but that's easily taken care of. I think it would be easy as pie.
Sub-games/minor objectives/mini-games:
Play as a pokémon; earn special items for playing mini-games as a pokémon in battle. The better you do at the game the more damage you inflict or debufs you cause. Can substitute the AI for a trainer's pokémon in the main game or act as a wild pokémon(to prevent this system from being abused/taken advantage of; how well you play determines the level of pokémon a player receives upon catching you or the amount of exp. upon defeating you).
Pokémon Contests/Musicals/etc. with new play controls to better take advantage of the hardware.(Musicals could be more like DDR or Dance Central for example.)
Cooking, while not a terribly huge part of the games, can also be implemented in a more fleshed out version. It has all of the ground work in previous games to work off of making it very easy.(berries, puffins, pokéblock, mushrooms, apricorns, etc...)
Mining from D/P/Pl can return for a little variety.
Breeding I think should take longer than just running around for a few minutes.
Developing a relationship with your pokémon can take on more meaning. Though X and Y seem to already be tackling this issue seeing it expand a bit would be nice. Taking out a chosen partner to walk around with you like in several previous games would be a great option.(Having a personality and/or friendship requirement before being able to do this is an idea to prevent absolutely everyone from doing this at once and causing problems, plus it requires more of a commitment than just "insert into first slot".)
^Any of the above can provide their own entertainment value, making battles the preferred, but not the only way to have fun with your pokémon or make them more powerful.(I recently heard of a WoW player who reached level 90 largely using means other than battle.) I remember in the animé an early episode where a vileplume hadn't ever battled before. Yet, when the time came to save it's owner it let out a *very* powerful solar beam. Do you now the reason they gave behind it's great power? Because she took care of it, and very well at that. That's something I would very much like to see be possible.