You guys aren't creative enough.
Idea 1: Make the computer a cheating cunt. Computer has more than 4 moveslots and always has the coverage moves to fuck you in the ass. Enemy trainers have variable teams meant to fuck up whatever you currently have. Random number generator disproportionately favors computer (such as computer stone edges always hitting or getting six crits in a row), basically make the whole game more like the Gen 3 battle tower.
Idea 2: Team rocket type badguys periodically steal your pokemon from your party. You must fight your strongest party member turned against you in order to get it back. You know how some RPG's have bullshit status like charm or shit like that? Just like that.
Idea 3: Dynamic enemies. If you start level grinding above a certain point, enemy trainers pokemon start leveling up too, so they are always 1 level higher. Their movesets match the higher levels too. Gym leaders are scrubs and use legendaries if you exceed this predetermined point as well. Once you break this point, you can't go back until you reach the next area.
Idea 4: Laws of Bullshit. Gyms have arbitrary laws like "No supereffective hits" or ones you can't even control like "No crits". Breaking the law causes your pokemon to instantly faint and permanently lose several IV's. Yes, its stats are permanently debuffed. Just like in FFTA.
As you can see, I've played some really bullshit RPG's.
