They should at least have the trainer do something more in battle than just give commands and use items; maybe fight along side the Pokemon? I'm thinking like Final Fantasy XI with the Beastmaster job right there; give commands with your Pokemon and fight along side them. Imagine a 'dragoon-like' trainer with a Charizard, fighting with a polearm to attack while the Charizard can help the trainer fighting by heating your lance to pierce through the opponent's hard defenses. It would be neat or a far stretch of imagination; that's what I'm doing in the Pokemon fanfic I'm writing. It's a mix of Final Fantasy and Pokemon...
I also wish that Pokemon would have ability and stat traits that relate to a Pokemon, kind of like that way the monsters in Tales of Symphonia 2: Dawn of the New World had. Like after awhile, a Pokemon could build up an immunity to a status ailment or type weakness. I'd also like for a Pokemon to have more than 4 attacks to use, but that's originally a part of the strategy that Pokemon was about...
OH, and Pokemon could have some sort of system wtih drop items. The items that some Pokemon may drop (like if you fight a Bellsprout, it may drop of vine, and the Trainer could synthesize it into an Escape Rope) could be synthesized into various items and trainers can also see if they can synthesize TMs and whatnot from various materials.
