Ruby/Sapphire would be okay. Just have a Game Corner and Dont... make.... villains stupid like in HG/SS. Emerald, I'm not digging the whole Rayquaza before the elite four, though I would enjoy elements from Emerald, such as multiple Wally battles and extra battles with May. Also, replace Wynaut egg with something intresting; maybe Chingling? So yeah, for the next DS system maybe, always thought that Ruby/Sapphire were underrated.
Something I would like to see: Have roaming Latias/Latios before the elite four. Those two: Fun to use. Peace, Ninja.
As for water routes: Wouldn't mind them as much if there was some variety. Add Azumarill, Corsola, Luvdisc, Recantlith and Chinchou and I think you'll be find. Really hated Dive feature too, but I guess I can deal with that.