I dunno if it's the least popular. It's certainly up there in the unpopularity charts, rubbing shoulders with FF2j and FF3j.

Why is it so unpopular? Probably because it took so long to release within the U.S., and even then, it still had "ugly 2D graphics" which modern videogame players didn't like. And since it was packaged with FF6, I guess it could've been overshadowed a bit too, I guess.