He will probably be a cutscene NPC, not unlike some of the storyline NPCs we see now. (Yda, Papalymo, NPC companion etc.)
Him being put in the Metalworks in Final Fantasy XI (in my opinion) was a bad idea because there was not much he could go in the ways of far from Bastok without it not making any sense. If you played A Moogle Kupo d'Etat and Shantotto Ascension, they make some creative workarounds to explain how "Moogle" and "Shantotto" are still in their respective locations and it came off kind of cheesy.
So I'm hoping Cid will make an appearance in the future of XIV, but as a cutscene NPC rather than one you can encounter in the open world.
Edited, Dec 12th 2010 2:31pm by UltKnightGrover