Now that that's out of the way, this show is pretty damn cool. Great characters and mostly great acting, the plot is certainly interesting and I don't think there has been a bad episode so far.
My only real issue with the show is it's just a tad too in your face theological philosophy. Now I've got no problem with theological discussions and ideas being presented in my tv and films. In fact it is really what sci-fi should be; idea based stories written in a pulpy, entertaining way. My problem with it is that they seem to not understand the point of atheism or atheists in general, now I'm agnostic myself but I was still a bit annoyed at how they handled atheist characters.
The most prominent atheist in the show is Dr. Gaius Baltar at the beginning of the series he mocks the idea of religion in a condescending and obnoxious way, and he starts talking about logic and reason as if it was some kind of replacement god. That's a trend hollywood atheism seems to have so I didn't think too much of it, but still that isn't how atheists think. But then it turns out (SPOILER ALERT) he's responsible for the complete and total destruction of humanity due to his own 'sins'. Now this still wouldn't be too much of a problem since the character is supposed to be selfish and despite being a genius quite short-sighted but the show wants to delve so much into his atheist nature as being the sole root of his flaws, it becomes a little offensive.
This is where the show seems to lack, throughout the first season Gaius Baltar goes on a spiritual journey in which he begins to pray, believe in god and in turn be a better person. This was just ignorant writing, and there is no excuse for that sort of thing. He did not begin to redeem himself because of his guilt and internal struggle with his dark secret, he changed because the gods showed him the way. The writers should have understood that atheists don't believe in a god not because they are afraid of being punished for their sins but because they literally can't believe in a god.
I can only hope in the following seasons there will be some characters who can debate the idea of religion without being arseholes.
TL;DR: Battlestar Galactica (first season) is a good show but doesn't understand atheism or atheists.