Can you please post more information about that hombrew/repro? I have never heard of it, and love Chrono Trigger.
I think what Mortal Kombat (PS3/360/PC) did would be an awesome thing to do with the game, or Link Between Worlds. Not a remake per-say, but a new game set in the same world with the same characters. Having time travel or multiple dimensions is a perfect avenue to reset the world and add a conflict. I would love to explore the original world and maybe new regions that were not in the old one - plus new dungeons and re-worked old dungeons. The possibility of this game gets me very excited, and while I am inclined to be negative with Squnix's output over the last ten years or so, games like Bravely Default, Relm Reborn, and Theatryrthem make me more confident in Squares ability to fan serve.