I've never seen Caprica, so I skipped over those parts, but here's some thoughts on NuBSG...
I don't think the Galactica God has as much of an influence as you think, twist. You compare it to Gandalf in Lord of the Rings, but there is a similar argument you could present for that. Gandalf dies after fighting the balrog, and then is sent back to Middle Earth as Gandalf the White to "finish his task". No other explanation other than "god did it".
Galactica God interfered by sending angels to help the humans and cylons complete their cycle and begin a new life. The only thinks we can say "god did it" about in the show is head six and Starbuck (the angels), while everything else is explainable. The head six and head Gaius had motivation to help each other out because they were speaking to themselves in a way. They knew the path they were headed for because they already experienced it and were sent back to guide themselves. Sort of like they're from the future, only their from a place where time doesn't exist in the traditional, linear sense. That's how I see it anyway, not too confusing once you wrap your head around it.
Also, I don't think anyone meant us to think the almighty Galactica God was simply playing a game with everyone's lives, or "waiting around" for something interesting to happen. I think it's more of keeping a balance between divine intervention and free will.
Lost was a very similar show to BSG, and in the end the "god did it" explanation was used even more in Lost than BSG.
So, other than head six & baltar and Starbucks disappearance (and them most likely being angels), what don't you like about NuBSG, twist? What else bothers you about the whole GOD thing?
Also, about the hybrid blood as a cure all thing, I have to say I never really thought about it much before now. I kind of forgot about that part of the story as it was happening. My guess would be they would have done more with it if it would have been interesting to do so. But if in following a line of events one or two plot points gets dropped along the way, I have to say I don't really mind. Like you said yourself, they thought about it, but it came out to technobabbley, so they dropped it.
I watch science fiction to be entertained, not to break down the technical aspects.