dang u joshnicerson, i just read the whole thread and got an idea for the realtionship feature and wham, u beat me to the post by a huge margin.
Anyways what if pokemon got a "chakra bar" like in Naruto GCN game, basically everytime you have your pokemon battle, every time he makes a successful hit his special bar will go up, any direct hits the bar will go down, but the bar would be a friendship/loyalty bar.
During fights if the bar is up high enough you can use "L/R" to dodge an attack if timed properly but would take away from your bar. If your pokemon is knocked out and your bar is high enough you would go into a button mashing mode or something to try and get up again, the harder the knockout the faster the mashing and the more the bar will get eaten up, or maybe use a ddr system which is used in Mega Man X: Command Mission, or Gladius, or if you don't know any of those games, Donkey Konga basically depending on how much damage the more buttons you would have to hit correctly in a short amount of time.
Also when the bar is higher attacks and accuracies are stronger.........and in due time you can upgrade attacks instead of learning new attacks i.e. Tales of Symphonia, so basically thunder wave = thundershock = thunderbolt = thunder. This is where when the bar is full you can choose between 2 moves that hasn't been learned yet, and the more you do them the quicker you learn them that way you have an option to learn what attacks, gaining levels would also add new attacks to your specials. Out of the battle it could activate certain specials such as Meowth finding money and items for you.
I think this would work well, because it would mean as trainers we really would be training them, that way just because a Charmander at lvl 15 doesnt mean that another trainers Charmander at lvl 15 would have the same stats or attacks! In further detail a lvl 30 Butterfree may have learned grass/bug attacks while another Butterfree may have learned psychic attacks and yet another that has learned a mix of the 2, as for TM's and HM's they would be put into the pokemon's special bar so they would have to actually learn them, no instant ramen here!
This would make the game more in depth, more of a challenge, and the multiplayer would be more varied. Anyways i have prolly confused everyone here but i would like to see what everyone thinks about it. Hope the long read was worth it!