Make a game in multi-languages (I saw Languages button in game options, but its still not working). I can offer my free services for Lithuanian language.
Add way to use mods for musics, sounds, graphics and others. I want use Anime Cries made by Arnie (I actually voice acted 4 5th Gen Pokémon), use Pokémon Reorchestrated and more.
Happiness by walking for whole Party. Because I now can't use my Budew when I always rise my Pokémon level when it reaches wanted Happiness level and now I even can't use my Furret with Headbutt 2k wasted... Same goes for a lot people actually.:P
Update Happiness system to 6th Generation standards.
Update Shiny rate to 6th Generation Standards.
Add breeding.
More suggestions/ideas will come later.