Well for me it's all follow up to his impromtu retirement speech in the mini-series and the questioning of whether humanity deserves to survive. That doubt shows through in his willingness to listen to Sharon making the same point in their conversations in the second season and in his ambivalence about the genocide in 3:07. He's the military he should be all for obliterating the enemy but he stands back and makes Roslin make the decision and won't prosecute Helo. These are just bullet points but I think they illustrate a more general trait, a reticence, a general with doubts.

I don't think we're supposed to believe that all this time Adama has been habouring the guilty secret that he "started it." Like Jane says below I don't think he interpreted things that way untill Bulldog came back. But I do think he saw shooting down Bulldog, using him as you pointed out in your review, as an example of man's inhumanity to man and he did know that the military weren't just sitting and waiting for the Cylons to come to the table. He had doubts, doubts about humanity's innocence, which I had thought might relate to the original war but this works just as well. Better. I think he jumped at the chance to take all the blame because it's actually easier to live with the idea that you're the one bad apple than go on suspecting that your whole society is rotten to the core.