Putting aside the changed mechanics (which probably would happen I'm this situation), things like this should be in).
-Each server is a different region, i.e: catch different, different map etc.
- You actually have to sleep, eat, and do everyday stuff or you'll end up in the Pokecentre (which would just become a different hospital).
-Cities will be "safe" zones while out on routes it'll be "free-for-all" and you'll have fight or avoid your way to the next town
-Put a level cap on certain areas so players with Lvl.100's can't go to Rpute 1 to pick on Lvl.5 novice trainers.
-Have a level up system for the trainers as well as the pokemon.
-More buyable items.
-The ability to chat (obvious).