Having seen the latest BSG episode, Downloaded, I have come to some ideas regarding the imaginary Six and Baltar we now saw in the series.
First of all, I find the similarities between the two imagined characters remarkable. Their gestures are very similiar, their way of talking as well. It is most interesting to hear the selfish Baltar talk about the suffering of humans and the like where as usually he is not affected by tha fate of others - especially clear in the scene where he is confronted with the fact that he betrayed all mankind and the first he thinks of is calling his lawyer.
This imaginary Baltar is not that way. He thinks more of the suffering the Cylons caused for everyone.
But most remarkably he speaks of God. Singular. While the roles of Six and Baltar seem to be reversed in "Downloaded", Baltar talks of God just like Six.
This made me think and I came to the conclusion that there might be some truth to Six' telling Gaius that she is an angel send by God. In this case the imagined Baltar would be an angel too.
I do not think this is literally speaking, but what if they come from the same source? I think they could come from a third power, maybe the one ( not unlike the original series ) that made the Cylons become self-aware and rebell in the first place. Maybe they are another alien species or something that try to make contact using this hallucinations or something.
At least I think there is more to them than just being imaginations. Just my random thoughts, anyway.