Some things I want to see in a R/S/E remake:
- I want the old player character to be a "secret trainer" in the game, much like Red in Gold and Silver. NPC's mention him now and then, and you can face him somewhere after the E4. Lvl 70 Pokémon or higher. (Possibly with a Groudon or Kyogre depending on your version.)
- Mystery bases are still there, but get expanded with wi-fi functionality (easy access friends list like the current PSS system and all)
- The world is still the same, but time has moved on. E4 has undergone changes and there are new gym leaders as well (maybe add a dark gym leader and make up a story why the gym changed to that type? Then again, the old E4 already had a dark type member). I basically want a remake where we play a new guy who has moved to Hoenn a few years after the original player character.
- As I mentioned above, time has moved on so we would need a new story. Not that these games are story heavy, but all of this is happening years after team magma/aqua almost destroyed the world with kyogre/groudon so we'd need some new events besides the gym leaders and E4.