I also vote for Skies of Arcadia. It is my favorite JRPG of all time. I would love to sail the skies there once more.
I'd also love to see Shenmue's story be finished, though to be honest, I'd settle for a movie, manga, anime, anything that tells us how the story ends. Just please don't leave us hanging.
Other titles I'd like to see get new or redone sequels:
Shining Force (I'd also like to see the Sega Saturn games only released in Japan released here)
Flashback (I've heard rumours of a possible Flashback reboot, hoping it's true)
Beyond Good and Evil (is that rumoured sequel ever coming?)