I would love to see Hoenn in upgraded graphics.
Ruby & Sapphire were very pretty games, and you could tell it took advantage of the GBA, so seeing it on the 3DS...
Oh oh and hearing the updated music would be love~
edit: really the only iffy thing about the game was that leveling spots were a bit lopsided. After Route 121, you basically only have the ocean to level up on until Victory Road. Which is fine for grass, electric, various neutrals but it sucks when you've got water-weak Pokemon to level up.
If they bring in the Match Call, but let you call people to set up rematches ala HGSS, that would help.
edit 2: Oh man.
Ruby & Sapphire with day/night cycles.