Disclaimer: I am only a little more than half-way through right now.

I think that Dr. Cid is the 'true Cid' of this game because (SPOILER)he has a connection to the airship through Balthier. Now, if this changes later in the game and Al Cid has a connection as well, I take all this back, but at this point, Dr. Cid is the only Cid who is related to the airship. All other Cid's in FF have been connected to the airship, so there.