I think it was carefully constructed so that there was no 'one answer', and the only way to do that was to leave it open ended. If they'd definitively said: "The angels were the forerunner Cylons of the previous cycle." then there'd not be a lot of room for discussion about it. But for me the 'explanation' came about when they time-jumped forward into our own contemporary era- we were the Cylons, and the humans- the entire argument of 'us v. them' was moot all along (which is not only very Star Trekkian, but was also kind of the point of the whole last half-season of the show), because we're all hybrids. Since we know Cylons can manifest as wholly digital entities, if we (and, of course, the colonists, as we know from the 'scorched Earth' they found) are ourselves Cylons, then they can present themselves to us to guide our evolution and try and avert the same crisis that's been repeated who knows how many times (which is why all the religious texts of the colonies are based around that theme). Kara was basically their equivalent of Jesus (or Gandalf, if you will).
But the point of the series is that we're the ones who broke the cycle. The reason all the earlier iterations of humans and Cylons destroyed themselves is because they never learned to work together and were incomplete without each other. It was only by merging into a single species -- us -- that they could transcend their fatal limitations and create an opportunity to break the cycle. We, uniquely among the iterations, are not doomed to repeat the apocalypse. We aren't guaranteed survival, we could still screw it up, but we do have a chance to avoid destruction and end the cycle forever, a chance that none of the others had.
That's another reason the finale made me like the series better. It makes it ultimately more optimistic. I never cared for its deeply cynical portrait of human nature, the way nearly everyone always made the worst and most selfish or cruel choices. But now I realize that what we were seeing was an incomplete humanity, a humanity that was more intrinsically flawed than we are. We're the outgrowth of the more positive, compassionate impulses that brought Helo and Sharon together and produced a hybrid race. We are the end goal that they strove for, the new form of humanity that can break the cycle and become something better. It makes the whole thing feel less cynical and misanthropic in retrospect, although I don't know if that would make it any more agreeable to sit through again.
The problem with the 'well it's all just metaphysical' explanation is that it just punts the explanation up to the next rung.
Only if you're thinking of it in terms of a science fiction narrative. If a story is overtly and intentionally a religious epic, then the existence of divinity
is the explanation. Many characters in this show kept telling us over and over again that divinity, destiny, and prophecy were real, and they were consistently proven right. We just didn't accept it because we made the mistake of thinking this was a science fiction show instead of a magic-realist space-opera religious epic. The finale proved to me that there was never meant to be a scientific explanation, that all those mystical things threaded through the series all along were meant to be taken at face value.
Sure, in real life I agree with you -- just saying "God did it" isn't an explanation for anything, just a way to avoid asking further questions. But a lot of fiction takes the existence of supernatural forces for granted and manifests them as real and tangible. There's no scientific explanation for Aslan in
The Chronicles of Narnia or Ares in
Xena: Warrior Princess. They're just gods.
I think what happened is that RDM looked at the DNA of the original show, thought about how to present the 'Ships of Light' arc in his intepretation, and realized that for his show it would make more sense if that 'third faction' from the show was presented as a seemingly-spiritual entity.
There's nothing "seeming" about it. It was the real deal. Glen Larson was a Mormon who based the original series on his theology. But as I said, network execs were uncomfortable with overt portrayals of religion for fear of offending someone, so Larson had to pass off his divinities and devils as hyper-advanced aliens. Moore was under less censorship, so he was able to use religion more overtly. He would've had no reason to half-ass it by throwing in a handwave about advanced aliens -- and no desire to do so, because that would've been the
Star Trek way of handling it and the entirety of BSG was Moore's aggressive repudiation of the limits he had to work under on
Star Trek.
But there's far too much congruence and specificity in what is presented to say that it was 'magical hoodoo'.
See, there's your problem -- you're pre-emptively dismissing the idea of magic and mysticism as something inferior and invalid. In real life, I certainly agree, but in fiction, fantasy and magical realism are as valid as any other genre. In a fantasy or supernatural story, magic or divinity can be portrayed with great specificity and consistency, because in such a universe, it is entirely real. The characters in BSG were quite specific that God, angels, prophecies, and destiny did exist, and the evidence consistently supported that premise and refuted attempts to debunk it.