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).
Also 3DS remakes/ports of SD2 through Legend of Mana, with various AI, balance, and bug fixes, because seriously those games were buggy as hell (especially 2 and 3 (emphasis on the 3)).
Elemental Gimmick Gear 3DS port. Because EGG is really good and like nobody ever played it and that's toooo bad :(
I'd be tempted to say an expanded version of Chrono Cross (with battle speed ups. Seriously why were Square's games locked at like 20 FPS????) with extra sidequests for the characters, but Square would probably do something peculiar like make Schala evil like in the CTDS remake (What even WAS the impetus for that?).
3DS/PSP/PC translation of motherfucking Sega goddamn Ages Phantasy fucking Star 2 fucking remake SHIT.
Minstrel Song-esque remakes of Romancing Saga 2 and 3, because Minstrel Song was a beautiful lady and I want to merry her.
also I think Soul Blazer should come standard with every new console released, sort of like how Dinwows comes with Solitaira.