ROFTL. You forgot your company name that I did never know we had. This should be my Signature Tommorrow.
Well, depending on what you have planned, I can suggest some systems that might turn up well in the game:
Catterpillar System ON/OFF -> The choice is yours. You can choose whether to let your pokemon walk along with you out of their pokeballs, or in their pokeballs. This should be orginal since it was only used in Pokémon Yellow with the Pikachu.
An Unique PokéNav -> We should try to create an unique Pokénav to give us a bit more of originality. Maybe some kind of N Gage, with phone, info about badges, wins, defeated trainers, pokémon status, and games like Pokésudoku, PokéSpaceInvaders, PokéSnake 2 (but with EKANS) or something would be nice.