>>26510731DexNAV is an absolute must. It was useful, and fits nicely into the RP of tracking and catching pokémon. Having it react to pokémon who were out in the overworld was a nice touch, too.
As for Amie, I could take it or leave it in its current state, though it'd be nice to have it expanded so it's more like pic related. Maybe have the new professor run a ranch like Oak did in the anime, and when you go there, you can actually watch them moving around/playing with each other. That's unrealistic, though, considering the additional animations you'd need for each pokémon.