However I think there is a great and simple solution, I hope. Remove the players and battling Pokemon from the world, or make them invulnerable, then overlay the screen with a battle scene similar to the classic game boy battles. We don't need the 3D terrain. It could be in a small dimension with a flat terrain and the players and Pokemon are immobile, and the camera is from the players perspective or 3rd person, and immobile. The player's Pokemon is in the lower right and the player sees the back of their Pokemon, the opponents Pokemon is in the upper left of the view port, and the trainer is hidden, or farther back.
The battle is also very slow with lots of "Waiting.." It seems like attacks should be able to be calculated and selected much faster and effects applied immediately, with someone who wants to follow closely can read the text before selecting their next move, while experienced players can mash on their next move and have it go right away.