WARNING: This post may upset readers who want to be lead on by President Roslin's irrational fears!
Now, at first I was skeptical of Commander Adama myself, but this just didn't add up. Of course, someone high up in the fleet is going to be a Cylon, but who could it be? Having the Commander be a Cylon just does not seem reasonable. All of the Cylons we have seen so far have not had children. They are in the same basic generation--about ready to have children, not about to be grandparents. If Commander Adama was a Cylon, he would have been replaced by one somewhere along the line. This would not have been too easy, seeing as he has been on the Battlestar all this time. If he was not replaced, then he would have had half-cylon children, and Lee and Zak would both be at least part Cylon.
The basic motivations for placing a Cylon in charge of the entire ship are sketchy, at best. This lead my chain of thought to the other Adama on board and in a command position. (Note: While Zak is an Adama, he died, this causes tension between the Commander, Lee, and Starbuck. It is highly unlikely that he will come back in a way almost
exactly like Ellen Tigh. That just would be irresponsible on the part of the writers.) Lee Adama is the perfect character to be a Cylon. Let's say he's somewhere between the age of 25 and 35. The Cylons have been gone for 40 years. That gives them plenty of time to replace the original with (or even to have made the original,) a Cylon. Having the original Apollo be a Cylon is actually fairly plausible--with the actors chosen for the new show, he looks nothing like his father. Ellen speculated in tonight's episode, "And I bet you look just like your mother." The mother we have never seen, even in a picture. Coincidence? I think there is more to the mother thread, if not in development of Lee's Cylon status, then for the sheer drama. Anyway, after 40 years, the Cylons come back and decide to wage war on the humans. Apollo returns and takes a command position on the only Battlestar to survive the original attack.
When Leobon shows up, Commander Adama tells Lt. Thrace to be wary of what the Cylon says, that there is always a
grain of truth with which he uses to sow the seeds of doubt. When Leobon tells Roslin that Adama is a Cylon, her thoughts automatically jump to the suspicious actions of Commander Adama, rather than anything Lee Adama does (her "adviser on the military"), who is more quickly thought of as "Apollo" than "Adama". No one thus far has suspected Lee, the true Cylon. Instead, they doubt the leader of the entire fleet.