>>20929759Story Mechanics wise:
Multiple routes, more side quests, and rival(s) who are more antagonistic and relevant to the story. For instance, lets say you have a mountain between you and the next town. You could take path "A" which is a tunnel through the mountain, which gives you access to certain pokemon and at the end you run into the bad guys scheming something deep within the mountain. Option "B" sees you going on a route over top of the mountain encountering different pokemon from what you'd see in the cave. At the end of the route, you get left cleaning up the mess from the bad guys and helping an NPC out but down't actually encounter the goons at this point.
Battle Mechanics wise:
I'd implement a Perks system similar to the abilities that many pokemon have, as a way to improve the balance. For instance some pokemon would get a perk that gives essentially gives them the "Levitate" ability, making them immune to ground type moves. Other perks might not have battle implications, but would make adventuring a little easier. For instance, a perk might give you a passive Flash effect in the overworld so you don't have to waste a move slot to explore a cave. Giving strong battlers these adventure oriented perks and giving weaker pokemon combat perks could help bring more variety to the battling scene.
Misc. Mechanics wise:
Multiple save files would be nice. It would be cool to be able to try out different teams and find the group that works best for you without having to reset all of your progress.
Multiple difficulty settings from the get-go would also be appreciated.