SO MUCH YES!!!-Expanded ocean routes; not in length or width, but in depth. I want to explore the seas from top to bottom, every last trench and crevice right down to the shadowy abyss. More ambiance, lighting effects, and visuals as well--I was a big fan of the underwater routes, they were and remain my favorite part of R/S/E. On the Gameboy Advance, they were of course rather plain, but on the 3DS, I'm hoping to see a real ocean on my screen.
And this would actually make exploring the water routes more enjoyable, other than things that you just have to do to finish the game.
Also, how about NPCs that can also dive, and you can battle them UNDERWATER!?
Thought of another one: no more HM moves. I know we've talked about it for ages but c'mon, now that TM's are infinite there is no need for moves that you can't erase without the help of a move deleter.
I think I've said this many times before, but I WISH HMs are replaced with Field Abilities, an idea that merges Riding Pokemon, Walking Pokemon, as well as HMs.