The Leveling system, when I think about it, also gives a way for players to just make estimates on how powerful a Pokemon is by looking at its level. I do like the specific stat training method, however. Sounds reasonable. Yet I was keeping some of the classic aspects of the game with the basic leveling system and experience requirements. And to be honest, I don't want to be oblivious to a Pokemon's power nor do I want to look at a large chart of its stats simply to get an idea. You gain a level and all your stats boost up by one or two points. Sounds irrational, but it's a tradition of the Pokemon games. Trainer skill just allows for leaderboards; to know which trainer is the best experience-wise and add healthy and unhealthy competition while encouraging fan-boys to follow them everywhere, haha.
As for manuals for moves...eh. Did they have manuals in the Pokemon anime? I don't even remember correctly...how did Pokemon learn new moves? "OOPS, I THOUGHT I USED A THUNDERBOLT, BUT OUT CAME A THUNDER" or some crap is how I remembered it.
I never really gave much thought as to how contests would work in a game. In the anime, they put moves together and stuff, but I'm pretty sure that would take too much time to work out and like you said, could be pretty graphics-heavy. But in the games, the Pokemon usually just threw out a dry move registered under some rankings like Tough or Cute and the judges ranked off of that, but that sounds pretty boring in 3-dimensions.
I also don't know how certain Pokemon will work with certain terrains. I guess you could take the anime route and just disallow land-type Pokemon in water or in the skies altogether, but that kind of sucks when you think about it, especially if you want to have a type advantage over a certain Pokemon. You could take the game route and transition into some random terrain to match the type of Pokemon you're fighting, but that still sounds sketchy. Like when you encounter a Flying type in the sky...do you transition on a cloud or something? When you encounter a Pokemon in the water, do you to suddenly find yourself standing on a hill in the middle of the ocean? Yeah, doesn't make much sense to me when I think about it either because both sound pretty bad.
Other than that, I like your input. You have great suggestions, but the things you questions I'm not sure about myself, haha.
@to the person who mentioned PokeMMO
I'm suggesting a live battling, anime-styled 3D version of a Pokemon MMORPG. One with all of the regions, also. I'm not sure if PokeMMO has anything beyond Kanto, but I've never actually played it so I could have absolutely no idea what I'm saying.