I'm tired of seeing a gym (all of them infact) that's theme is type based. This makes the game stupidly easy for those of us who have been here forever, and do not provide a learning curb to the new generation, it only grinds the "X type beats Y type so find a pokemon with X type to beat the Y gym" concept into people's head, which should already be made an important part of the game at the start: where you fight your rival with the X to your Y. I would like to see gym themes that are more dynamic, and here are a few:
Double Battle (done as the 7th gym in Hoenn and worked quite well)
Stall-based team
pure sweepers
pokemon that have breed-only moves (such as Curselax, Bellyzard etc)
Baton-pass team
Hazard-teams (stealth rock, sandstorm, toxic spikes etc)
the list can go on as people think of more intresting strategies. This will help teach noobs interesting styles of play besides the typical idea that leveling your starter to 100 and owning everything with 4 attacks is an actual good idea.
Personally, i would like to see a hard mode of some kind. While this idea would absorb much of the chip-space i feel that it would keep us pros and people who will be transfering 4th gen pokemon from becoming very bored with the story/plot (as its always the same stuff). Being rewarded for playing on this mode wouldnt be too difficult. Just give us a pokemon(s) with unique moves after we beat the game. Such as a surfing pikachu, Banette with shadow force, etc.
also, i want HM's to completely disappear. The only hack i ever use in the main game is the walk-through-walls hack because im tired of stupid HM's that dont contribute anything to game play and only hamper the experience. We are all forced to have a Water-type (almost) due to surf, waterfall and other idiotic water-HM's. Also with the useless Cut and Flash it forces your pokemon choices unto you, which is VERY counter-productive to what the pokemon games are about: customization and personalizing your critters.
Lastly, i'd like to see a more efficient way to move between cities I've already visited. Agian, i'm forced to have a flying-type on my team if i want to get to past-cities without backtracking for long periods of time (some times requiring HM's) This combined with Surf/Waterfall we are actually only allowed 4 pokemon in a sense. Sure, some pokemon both surf and fly but why would you teach it surf, waterfall and fly? (and mabye whirlpool AND/OR dive?) My point is that it's a complete contradiction and an extremely outdated system of progressing the main character in the direction the game-makers want him/her to go. Get. Rid. Of. Them.