There's still the question of how he survived the water blast. Six didn't; and it's really stretching the suspension of disbelief to say that Six - who was a Cylon infiltrator, which seem to be much more physically durable and capable than human counterparts - did not survive the impact, while Baltar did.
Plus, Baltar's eyes were burned out by the nuclear flare. Yet he was left with no more than some scratches (Hmm...six's scratch in this episode) and was able to see perfectly fine, and somehow managed to turn up with the crowd of people near the Raptor - even though it seemed that Baltar's home was isolated from pretty much everything else. You'd think that he would've suffered some broken bones, at least.
Finally, there's the deal with Six and Baltar being in each other's heads. Although they both seem to be fantasies, reinterpretations of the character to stress the characteristics that the host found most attractive.
According to the BattlestarWiki, Baltar was shielded by Six' body - specifically, the blast wasn't strong enough to totally destroy his house, and he was blown out the other side (so to speak). Also, it's not explicit his eyes were
hurt - his 'ouch' could be simply down to shock (albeit still raising questions about looking into a nuclear blast and all that). This, of course, is open to retconning. If Baltar was a cylon, though, Six was rather pointless - they didn't need an infiltrator (Baltar would have internal code in his noggin to booby-trap the CAP), or lover (as cylons appear to need to use humans to reproduce; and there's no reason for Six to ever meet Baltar otherwise). Plus there was no point in Six explaining human-cylons to him.... the only reasoning would be plan the Galacticas' entire escape, which seems rather at odds with firing nukes at the thing.
EDIT; (
http://www.battlestarwiki.org/wiki/Downloaded)
In the Miniseries novelization, this is expanded upon; his house wasn't entirely destroyed (that is, not reduced to pebbles) and when Caprica-Six blocked the blast with her body it shielded him enough; he was thrown through the house against a wall and slightly hurt but did not die.
An interesting thing in the miniseries was Baltar speaking of wishing to do AI research, which was banned after the Cylon war. I can't help but wonder if it is related to the virtual Six.
(really stupid idea; Six got 'into' Baltar as some result of the nuclear blast; inhaling self assembling nonotech that built pathways or something in the brain - this would seem far to technobabbly for Galactica, though)
Incidentally, why the hell do I read these threads? Sky One's only up to Home, Pt2.........
