Warning! I am advocating a smaller, downloadable game, not some big-budget effort. For business reasons, and for reasons of pragmatism, it would be the ideal route to take. Like I have said in another post, there is no reason why SE can't be a company that pushes out smaller FF spinoffs (that aren't low effort minigames or All The Bravest ripoffs) in between their AAA projects.
A new 2D Square RPG should be on as many platforms as possible. Don't needlessly leave anyone out and timidly purr when asked for the reason that there's any kind of extra cost or effort involved. Take the indie route and don't restrict it to only a tiny handful of platforms; go maximise the audience, especially if it is a downloadable game where concerns about shipments and supply chains are null. Square recognises the existence of Steam now, and is steadily releasing content for PC (even if the reason for putting the FFXIII trilogy up on Steam is for an ulterior reason), so maybe they are learning that lesson.