So yeah, I guess if they just use the 3D to separate the forground and background (Opponent and Player in battle) and kept the sprites I'd be fine with a 3D remake, I'd love to see the cuscenes in 3d.
In particular I hope they take some elements from Emerald story wise.
Such as magma and aqua BOTH causing trouble, magmas base being in the mountains, and the stories legendary getting its own dynamic cut-scene.
Basically the emerald storyline up until when one of the Legendaries is awakened, then the story should follow its versions plot. But when Kyorge or Groudon wake up and just before you fight it I'd like there to be a scene during those two points.
Another thing I'd like them to add is a story to the Battle frontier to make me want to go further, like they did in Gold and Silver for the Gym rematch and in Diamond and Pearl with Lucas' father.