Brad, you make an excellent point that Leoben mentioned that "Adama is a Cylon" without specifying WHICH Adama, father or son. We already know that Baltar's "Cylon detector" is useless when dealing with these special final five Cylons (otherwise it would have detected Tyrol and Tigh, at the very least) so from that point Lee is still a candidate for the final Cylon. Further, Apollo has had a quasi-messianic streak that has shaped the survival of the human fleet from the very beginning. Consider:

During the miniseries he sided with Pres. Roslin against Adama and wrangled together those human ships with FTL capabilities which became "the fleet" thereafter.

At the end of season one he sides with Pres. Roslin against Adama (again) to protect her presidency and (indirectly) helping her mission to find the Tomb of Athena.

At the beginning of season two he aids Pres. Roslin escape from Galactica, and allowing her and her followers to jump away to Kobol and thereby (directly) furthering her mission to find the Tomb of Athena. Once in the Tomb of Athena her points out the importance of the Lagoon Nebula and its importance as an astronomical marker on the road to Earth.

During the attack on the Resurrection ship he has a strange (and as yet unsatisfactorily unexplained) death wish after ejecting from the Blackbird. His vision of floating on the water while waiting for death to claim him was suggestive of the resurrection process of humanoid Cylons as well as the "vats" in which the baseship Hybrids operate.

At the end of season 2 he urges Adm. Adama to make the fleet jump away once the Cylons arrive on New Caprica thereby saving the remnants of the human fleet once again.

At the beginning of season 3 he disobeys Adm. Adama's orders (for the Nth time) and jumps into the fray to help Galactica in the exodus of the Colonials from New Caprica. Sacrifices Pegasus and in so doing ONCE AGAIN ensures the escape and survival of the Colonial fleet.

At the end of season 3 he appears to be the only one to see Starbuck and hear her message of her journey to Earth.

I don't know if I'm just reading more into it than is there but it does seem, IMHO, that Apollo's character has been central to both the survival of the Colonials and their quest to find Earth. Curious also that his call sign is the name of one of the Lords of Kobol, right?