This will probably be locked... But I would really like to see the Rainforest route revamped heavily with the DS's (or DS Advance, w/e) 3D graphics. And Fortree. It would be great if the trees were very, very tall, and you could see shrunken versions of the general area. Fortree would definitely benefit from 3D.
Dive would also be great, if remade. It could be 3D, and you could control your trainer by touch screen. Think Distortion World, but you have free control so you can go in any angle.
Hoenn, though the games themselves were my least favorite, is a very beautiful region. The volcano would be amazing in a remake, and so would the cutscene to get on top of it.
If they followed the Emerald Route, Kyogre vs Groudon could be great. There are 3D cutscenes in HGSS, so I take it that there would be some in LRSS (LandRuby/SeaSapphire?) too.