Many of the suggestions to improve the story or your interaction with your avatar and your Pokemon sound good but none of them address the problems with combat which is in my opinion two simple. With one Pokemon getting Approximately one move, with no movement at all making any allowable depth purely mathematical and not tactical.
Their are two directions I can see you going with the combat to improve it. The first if you want to keep in the standard structure of the game is to go with action combat and allow you to directly control the Pokemon. That probably makes if a have appeal to a different type of gamer than the current fan.
The other option I see working well, possibly just because its what I would love to play(not that I would not enjoy action Pokemon.[Lets make it an aside inside and aside inside an aside.]), would be Pokemon tactics. Gird or distance based turn based battles on a field with multiple Pokemon fighting at once.
Their are two directions I can see you going with the combat to improve it. The first if you want to keep in the standard structure of the game is to go with action combat and allow you to directly control the Pokemon. That probably makes if a have appeal to a different type of gamer than the current fan.
The other option I see working well, possibly just because its what I would love to play(not that I would not enjoy action Pokemon.[Lets make it an aside inside and aside inside an aside.]), would be Pokemon tactics. Gird or distance based turn based battles on a field with multiple Pokemon fighting at once.