Get rid of...
HMs: just make them deleteable, its just plain annoying. Rock smash must die as well, or something cool like do as much damage as the level the pokemon is, to restrict power on weak pokemon but still be useful the rest of the game
TMs losing PP, yeah itd make some moves neverending but would anyone really care?
Add...
GYM rematches: you go to each gym, with updated puzzles and the entire gym gets stronger trainers.
Many more triple and rotation battles. It was cool but there were only a few....