There is so many things that can be done....
All regions - perhaps this could be a project for the 3DS, this may take a long time but one of the things I loved about G/S/C was the fact that you went back to Kanto. It would also be pretty cool if we got regions from console games such as XD too.
Stop getting rid of features - If Battle Frontier was in Platinum, why not Black and White. Battle Subway was just Battle Tower fancied up. The VS seeker should also return, the elite four gets very boring after a while. Following Pokemon could return too. Basically, whenever there is a new game, there shouldn't be too many features missing from the last game. In Pokemon B/W's case, the game has a lot less to do than Platinum.
Customisation - Trainer Sprites could be customised as well as stuff like the secret bases introduced in R/S/E, records should be able to be mixed online with random people so you can find them in your world.
Battle Tower Styled True Elite Four - I suppose this would only work if there was multiple regions, to become the true champion you should be up against either lvl 100 pokemon or be able to defeat the strongest trainers in battle tower leveled style. Perhaps even Battle Frontier could determine whether you are strong enough to be the champion or not.
Fight back against hackers - This means no asking for ridiculous trades on GTS and stronger protection online against hackers. It will never be perfect, but if GTS gets fixed and hacked Pokemon can only be as strong as legits, then it is fine.