I personally think it will happen because in 2013, it will be a decade since the Ruby and Sapphire releases, much like how Gold/Silver had a remake 10 years later. If they're gonna do a Ruby/Sapphire remake, they should keep everything from the previous game, and include stuff like Emerald's Battle Frontier, and I think it would look amazing with updated 3D graphics for the Nintendo 3DS. If you don't like the idea of 3D models and the game being for the 3DS, you can just play the gameboy version, which would have little difference gameplay-wise.
3D models aren't gonna happen I guess.