I want them to KEEP the sixteen gym and going to Kanto thing, because that's extremely fun to do in the game. I also want them to KEEP Red in the game, as he's my favorite person to beat (plus I want them to keep the music for when you're facing him, because that music owns my soul.)
Knowing the people who make the games, they'll probably add the new pokemon. HOWEVER, I would like it to be after something, perhaps the final battle with Red. Or perhaps even after you complete the pokedex of the first 251 pokemon. That was, you aren't thumped with having 492 or something Pokemon to chase after at the beginning of the game, and you still have to only chose from the firse 251 for your team. (Because we all know we miss having less to choose from, so we pick pokemon we have never had before to not have the same team as in every other game. :3 )
Main battles need to be stronger too. Even Red was really quite easy once I got the hang of it. I also think that Red should have the team that Red has in the Manga, but that's just me. >__>
There are more that I want, but I'm going to stop here for now because I'm tired. :3