Think of it like this. The purpose of the game is exploration, so try to make a protagonist that is focused on that. In Zelda, Link was a bumpkin exploring the grandiose nature around him. But with Pokemon, we are in modern civilization, at least that is how I feel. Maybe make it a past game, with someone who hasn't seen much of the world around him. Like a wild boy, or maybe a Pokemon.
Wow that surely was original, you should hold on to that idea till got thw skills to start on yournown game.
Sadly though I already have the main character's tale planned out a bit. I'll send you the files tomorrow (im on my phone now and its really late here) the bulbasaur idea is really cool too, you won't get him as a starter though. He's obtainable in an early exploration quest where you have to locate the hidden gardens.
I was thinking about new field moves as well, problem is, they're kinda hard to implement XD.
Anyway, I have an old game thread up, its called fiesta meets freedom. This game is based on that one.