I don't anticipate any dramatic changes to the gameplay of the main RPG series. They've kept it for the past decade, and they barely did much to it, yet the franchise is still highly successful. Hell, Pokemon's system is hardly that different from the original Dragon Quest, a franchise that's still amongst the most popular in Japan. It's kinda like the saying "if it ain't broke, don't fix it", so Pokemon's not liable to change anytime soon.
However, spin-off games like Mysterious Dungeon are great alternatives to playing with all the Pokemon. More games like that should be highly considered after Diamond/Pearl's released (for that matter, they should make another Mysterious Dungeon game somewhere down the line to include the 4th gen Pokemon, or even the 5th gens if they make one). Also, the fact that physical contact is finally being added to Battle Revolution puts a fresh, graphical spin on a staling system while not drastically altering the mechanics behind it (similarly, as with the afforementioned Dragon Quest, Dragon Quest VIII allowed you to view your characters actually hitting the enemies after years of battles only being viewed in first-person perspectives).