A Star Ocean 2 full-blown remake with SO4's battle system, which I was quite partial to.
I'd love for a Vita compilation of the original .hack quadrilogy, as well as Arc the Lad 1 & 2. Perhaps just combine 1 and 2 and make it just one seamless game.
And I don't care what anyone else says, I'd love a Baldur's Gate remake. Both 1 AND 2. I'd still want it to be isometric, but with updated graphics and perhaps added features.
SaGa Frontier 3DS remake. Re-implemented Fuse quest. Re-add Blue's original ending. Plus some new (character unique?) sidequests to make up for the other cut content (which really needed to have been cut, judging by the Ultimania guide).
I agree with Mesh's suggestion as well. A SaGa Frontier remake would be wonderful for a handheld.