Do:
-Make trainer customization more than just a few accessories.
-Have trainers look different from others of their class. It's weird that all Youngsters, Lasses, Beauties, and everything else look the same. Like, Team Rocket all have the same hair color. WHAT??? At least colors should be changed.
-Kingdra --> Sea Beast with Dragon/Water typing. Like, 1/2-Gyarados and 1/2-Kingdra
-Double Triangle of types (Fennekin Fire/Psychic, Froakie Water/Fighting, Chespin Grass/Dark)
-Raichu Fairy/Electric-type
-Make Champion more like Blue/Gary in the sense that they aren't all helpful and friendly. Actually, a character like Hugh+Wally would make a great champion. Determined (Wally), a bit cocky (Blue/Gary), and hotheaded (Hugh).
-Cameos such as Ethan and Brendan, because they never showed up as an NPC (except as a rival in Brendan's case), and also, include Kris or Lyra somewhere. Actually, having Kris as a character would be really cool (but unlikely). But still.... it would be cool to have her somewhere, even as a minor cameo (PWT-type thing).
-Make all Kanto/Johto/Sinnoh/Unova starters available.
-R/S Remakes.
Don't:
-Make battle intros take forever.
-Mess up Litleo+Evolutions with crappy moveset/stats/etc.
-Jack up the trainer customization thing.