Okay, many things that I'm going to say have been said. So tuff. Deal with it.
First, I would add Kanto and Johto. Yeah, that would make the game much longer. And more fun. R/S/E weren't all as good as they were claimed to be. They were supposed to be the longest set of games for the Pokemon series yet, but I think that G/S/C were a lot longer.
Second, I would add all the Pokemon in there from the other two regions plus those from Hoenn.
I would change it so that you can choose where you want to start out in. Like, at the introductory menu, it will ask you if you are living in Kanto, Johto, or Hoenn. Then, you could travel throughout the whole /known/ world of Pokemon. Besides Orre. But that'd just be stupid.
Also, I'd add morning, day, and night settings. And also DST to suit the consumer's personal time zone! :D