Pokemon feels like it was never really meant to be an RPG. I mean, why do all the bad guys in the game feel that they can overwhelm you by beating your animals instead of just kidnapping you or something? It makes them seem less humane and much less evil.
Why not have a bad guy that actually wants to hurt you and not make you cry all the way back to the Pokemon Center? Why not, then, use your Pokemon to defend yourself--to which the baddie responds by throwing out his own Pokemon to create a fair fight? I honestly wouldn't mind seeing the trainer get hurt. It adds to the intensity of the world. It's no fun getting to see Ass Ash ride his Charizard like a dragon but not be able to do it in the videogame. Full-on action adventure world work perfectly with this and, instead of going around getting badges to be the champion of... Pokemon, I guess even though there are still plenty of trainers still better than you, why not have a significant threat like in Ruby/Sapphire or Diamond/Pearl where some serious shit was at stake.
...
On a completely different note: am I the only one who thinks HMs should be done away with? They're an incredible nuisance and they distract from fully customizing your team since they take up a slot and you can't explore/fast-travel without them. Why not have HM's be taught through special minigames and just have them be acquired as skills instead of actual moves?