Why you don't want gods in your fiction
I won't deny that some of my distaste for the religious ending comes from my own preference for a realistic SF story, where everything that happens has a natural, rather than supernatural explanation, and that this comes in part from my non-religious worldview.
Nonetheless, I believe there are many valid reasons why you don't want to have interventionist gods in your fiction. God should not be a character in your story, unless you are trying to write religious fiction like Left Behind or Touched by an Angel.
The reason is that God, as we know, works in strange and mysterious ways, his wonders to perform. We don't expect to understand them. In fact, there is not even a requirement that they make sense. Some even argue that if you're going to write authentic fiction with God as a character his actions should not make sense to the characters or the reader.
The author of a story is "god" in that they can write whatever they want. But in real, quality fiction, the author is constrained as to what they will do. They are supposed to make their stories make sense. Things should happen for a reason. If the stories are about characters, things should happen for reasons that come from the characters. If the story is also about setting, as SF is, reasons come from the setting. Mainstream fiction tries to follow all the rules of the real world. SF tries to explore hypothetical worlds with different technology, or new science, or even ways of living. Fantasy explores fantastic worlds, but when done properly, the author defines the new rules and sticks to them.
But if you make a divine character, even an offscreen divine character, you give the author too much power. They can literally write anything, and declare it to be the will of god. You don't want your writer able to do that. You may want them to be able to start with anything, but once started the story should make sense.
As BSG ended, Adama and Baltar describe (correctly, but not strongly enough) how improbable it is that evolved humans can mate with the colonials. In reality, the only path to this is common ancestry, ie. the idea that humans from our-Earth were taken from it and became the Kobolians. But Baltar is able to explain it all away in one line with his new role as priest, it's the will of god.
In a good story, you don't get to explain things this way. You need to work a bit harder.
Now, if you absolutely must have a god, you want to constrain that god. That's not too far-fetched. If you were writing a story in Christianity, and you depicted Jesus torturing innocents, people would not accept it, they would say it's at odds with how Jesus is defined (though Yaweh had fewer problems with it.) BSG's god is never defined well enough to have any constraints.
He,and his minions, are certainly capricious though. Genocides, Lies, Manipulations, exploding star systems, plotting out people's lives, leading Starbuck to her death to achieve goals which could easily have been done other ways. Making that cycle of genocide repeat again and again until random chance breaks it. Not the sort of god we can draw much from. (One hopes if we are going to have gods in our fiction, they provide some moral lesson or other reason for being there rather than to simply be a plot device that explains things that make no sense.)
In literature, bringing in the arbitrary actions at the end of a story to resolve the plot is called a Deus ex Machina and it's frowned upon for good reasons. The BSG god was introduced early on, so is not a last minute addition. People will disagree, but I think the divinely provided link to real Earth is last minute, in the sense that nothing in the story to that point tells you real Earth is out there, just the rules of drama (that the name "Earth" means something to the audience other than that ruined planet.)
If you want to write religious fiction, of course you can. I'm less interested in reading it. Moore said he did not intend to write this. He wrote the miniseries and made the Cylons monotheists and the colonials polytheists (like the original) and the network came back and said that was really interesting. So he expanded it.
But he expanded it from something good -- characters who have religious beliefs -- to something bad. The religious beliefs were true. But they were some entirely made-up religion with little correspondence to any Earth religion (even the Buddhism that Moore professes) and as such with no relevance to the people who tend to seek out religious fiction.
Giving religions to the characters is good. It's real. It's an important part of our society worth exploring. However, resolving that some of the beliefs are correct, and bringing in the hand of god is another matter.
More loose ends
- The Colony had several base ships. When it started breaking apart, base ships full of Cavils, Dorals and Simons should have jumped away. What happened to them, and why won't they come a calling soon? (God's will?)
- Likewise, a force of Cavils, Dorals and Simons was invading Galactica and was in a temporary truce when fighting broke out again and Galactica jumped. What happened to them. In particular, since the first Hybrid predicted the splintered Cylon factions would be joined together again, why didn't they?
- We never resolved why the first Earth was destroyed 2,000 years ago, and that this was the same time as the fall of Kobol and exodus of the 12 tribes. Was this just a big mistake and all 13 tribes were supposed to flee at the same time?
- I don't know for sure about 150,000 years ago (it comes and goes) but 135,000 years ago the Sahara was covered by large lakes.