Threads of Fate and Vagrant Story are my top two choices of needing sequels.

As much as I love Xenogears, I feel the game is pretty self-contained and wouldn't need a sequel or even a prequel (though playing as Lacan would be kick ass...) but since most of the Xeno team is gone, it would probably feel like a shell of its former self.

I also need to do a shout out for The World Ends With You. Its also pretty much self-contained but a sequel revisiting the world and its gameplay mechanics would be awesome, not to mention its one of the first JRPGs I've played that would really kick ass with co-op.