Something cool they could do (but will never do) is make a game for a platform with graphics like FF. They can have the trainer run around like the FF games and encounter random battle the same way, and in the battle you can control the pokemon in a 3d battle field and have 4 of you move set to 4 button on the controller. (and in the main menu you can assign any of the moves you've learn in the past to the 4 attack slots)
But making 3d movement for all the pokemon and the attack animation would take alot of work not to mention the full 3d world, different types of battle fields, the peolpe in the game, and cut sences.
I bet even the poeple of Final Fantasy would have trouble making a game like this.
Finally, the main problem is that the Pokemon games are targeted for kids not older teens.