I think the in theory ending: settling down and blending into a world, is really where the series was heading and was the best ending they could give to this human struggle.
On the details though…
The whole God stuff was just a mess. I’m down with the idea of God playing a part, but as others have noted, it really seemed more the like the concept was used to fill in plot holes quickly rather than being a thoughtfully crafted plan. Making the head creatures be angels seemed to be largely arbitrary to the plot and just bizarre, if that’s what they were. The Thrace as angel thing just wasn’t well couched or set-up. “Daniel” felt like a throwaway explanation for the model # discrepancy.
It’s not even clear why there needed to be a final battle in the first place. Did wiping out the colony wipe out the “bad” Cylons? No: it was established that baseships were jumping in an out of the area regularly, and we saw no baseships appear or get destroyed in the finale. Did the “bad” Cylons learn anything? No, they got double-crossed and blowed up. So once we had both Hera and angel Thrace on Galatica, we already had everything we needed to head to “new/old/good” Earth and get exactly the same ending.
Also, from the perspective of the crew why was Kara the only one who could put in jump coordinates? I mean, in the time it took, Adama could have just crawled over there and punched some in himself. And since jump coordinates are just a string of numbers, you’d think they could just pull up a favorites list or something! I suppose it might have been important that the ship not jump to the middle of nowhere since it might never jump again, but as we learn soon after, they can just send a Raptor to meet up with the rest of the fleet who could then come back and ferry them off.
The problem I have with this is that it didn’t actually play into anything. The fact that Baltar and Six take Hera, and Athena and Roslin lose her in the opera house, has real emotional resonance: it seems like a big tragic turning point: something that makes all the difference. But it wasn’t. It was a prophecy basically of just one of any random arbitrary events that happened in the final that happened to lead towards the end. They might as well have all had dreams paralleling Adama breaking into mantears and whitewashing his wall the entire series.
That’s because nothing that happened in the opera sequence was actually permanent or necessary to actually get to the end. Roslin and Athena were not cut off from Hera forever: they caught up to her and everyone else like, five minutes later! There was no real significance to Baltar and Six taking Hera: sure they took her to the CiC, but she could have just walked there on her own. Baltar was critical to getting Cavil to stand down, but he could have simply gotten there himself separately, or been there. The prophecy happened to mirror the five standing there… but again, so?
It felt more to me that the original intent of the opera sequence WAS to itself be a major turning point in things… but they decided to plot things out differently and so just sort of tacked it in there. I loved the mirroring, but it just didn’t play into anything that paid off as promised.