What features do you want in the next PMD installment?
An EV/IV system like that from the main games. I cannot imagine how the EVs would work but IVs can probably be randomly determined from the dungeon you recruit said pokémon.
Something akin to the Battle Frontier (a sort of proving grounds?) where you can dungeon crawl under very specific conditions and win points that you can trade for unique items and maybe moves to be tutored.
I will elaborate on the Battle Frontier idea later on.