Well if you don't already know, Game-Freak's Junichi Masuda tweeted: "Thanks for your thoughts. Ruby and Sapphire are important games to me. I will consider your request." Of course this isn't confirmed that Game freak will be making this BUT if they do here are my thoughts.
1. No black and white Pokemon, they suck.
2. They should be 3DS games.
3. Let your Pokemon walk with you.
4. MUDKIPS!
Lets hope for the best!! - chang