I agree with Xous and psyburn's mention of the game's pacing being too slow for the simplest things, but as for what I would LOVE to see are as follows...
1) More Pokemon! like another 150+
2) Some pre-evolutions.
3) Eeveelutions (Mainly, dragon, flying and fighting)
4) NEW Starters. I'm tired of the same three. Fire, water and grass. yeah I know they're a theme but still! lets see some change. like a Dark, Psychic and dragon.
5) New Types! add some more variety to the game, i.e. Light, shadow, void.
6) ABSOL EVOLUTION!!!!
7) more Multi evo lines, i.e Gardy/Galade
8) better legendary Pokemon, more classic and cool, like the 3 dogs, Raiku, Sucian and Entai. (Not a pink and blue dinos. i.e Dialga, Palkia.)
9) a better storyline, with NO EVIL TEAMS ATTEMPTING TO TAKE OVER THE WORLD!!!!!!
10) more challenging E4s (frankly the current ones are WAY to easy.