Wow, this part of the rewatch has been the most fun yet–it’s amazing how differently many of the scenes in these early S3 episodes play now that we know how S3 ends.
Fat Lee is more distracting than he was last time around for me, but that might be because of the order I watched the series. The first episode of BSG I ever saw was “Occupation/Precipice,” and I knew nothing about the series except a brief plot overview and character list that I read online after hearing about the show’s critical acclaim. Hence, I didn’t know that the actor playing Lee was wearing a fat suit in the early days. It was a very pleasant surprise when he started losing weight so fast later on in the season… 
Poor Ellen. It’s too bad that she didn’t feel she could trust the other resistance members to tell them about the threat to Tigh; they might have found a way to get him into hiding. Was she afraid that she’d have to admit to how she’d found out the information, or did she just not have any faith that the others would put Saul’s safety at as high a priority as she did?
It’s ironic that, in the scene between D’Anna and Athena, both of them are telling the truth, yet neither believes the other. Hera is alive, and Adama wouldn’t (and didn’t) lie to Athena, since now we know he didn’t know about the baby swap.
Speaking of babies, the first time around, Athena’s comment to Tyrol for Cally to never let their son out of her sight just seemed like concern for the Tyrols and lingering doubts about Hera, but now it’s even stranger, since Nicholas is the second born of the new generation. Athena can’t consciously know that Tyrol is a Final Fiver, but could she know something subconsciously and it’s glimmering through the repression just a bit here? Or is it just a really, really big coincidence?
The biggest question of all that this episode leaves for me is in the scene between Anders and Roslin when they’re talking about Mya and Hera/Isis:
Anders
I don’t suppose you’re going to tell me what this is all about. I mean, what’s so important about this kid?
Roslin
She may very well be the shape of things to come.
That’s either a blessing or a curse.
Now, it seems like we know what’s going on here: Roslin wants Anders to protect Hera at all costs because she’s the Cylon-human child. But wait a minute, “the shape of things to come?” Where did that come from? The only other people we’ve heard that phrase from are Head Six in the Opera House and Head Adama (or Vision Adama?) in Baltar’s dream/hallucination on Kobol when Adama drowns the baby. Where is Roslin getting this from? Is it scripture? Is it from a vision? Has she subconsciously already been to the Opera House somehow?
Also, it’s interesting that although Roslin wanted to abort Hera to keep her out of Cylon hands, she doesn’t authorize Anders to kill her if it looks like they’re going to be captured. Roslin seems to have gone from being out solely to keep the baby away from the Cylons at all costs to trying to protect the baby from the Cylons–and there is a difference. Why the change? Is it because Roslin has Hera’s blood running through her veins and is now somehow connected to Hera’s fate? Is it because Hera could be “either a blessing or a curse”? A blessing or a curse to whom? And how does Roslin know this?
A lot of viewers have been predicting that “the shape of things to come” is the integration of Cylons and humans, but that’s in part because we’ve been knocked over the head with this idea of Hera being so important and “the shape of things to come” for a long time from Head Six; it doesn’t make sense for Roslin to draw that conclusion on her own. It’s not a really logical conclusion, when you think about it. For instance, just because a tiger and a lion mate and produce a liger, that doesn’t mean all zoologists jump to the conclusion that the liger is going to be “the shape of things to come” for lions and tigers; yeah, maybe you’ll get a few, but on the whole, most cubs are still going to be lion cubs or tiger cubs. Not the greatest example, but I hope it shows why I’m curious about where Roslin is getting her ideas about Hera’s destiny from.