It's not a hack, first off. RMXP game. Heh.
You have some good suggestions, but I don't follow the TV show much, and I certainly don't want to base this around it. I already have the champion worked out, anyway, he's an original character, and more along the lines of Lance (in GSC, not RB) and Steven, he's actually in the game and plays a story role, but a rather bigger one.
Also, I don't think that I'm going to have a name choosing thing at all, and I don't think that I'm even going to call him Samuel (the name was invented in the show, never mentioned in the games. I don't deny that his name is Samuel, I do of course go along with that, but I feel it's not necessary). His name'll be Oak, and hers would be Agatha.
As for choosing a boy or girl, not possible. This game has a storyline, unlike most pok?mon games, and while for the most part the story is very nonlinear and traditional, aspects of it are about the main character (Oakie-boy).
Thanks for your suggestions, though. ;)