There were a few rough patches at the start but the real cracks in Battlestar Galactica started to show (just as they implausibly would later in the diegetic ship) in season three. More and more emphasis was placed on destiny and prophecy and dream visions until the show started to slip out of science fiction. Heavy-handed stories didn't help. They re-made the Babylon 5 episode about a doctor who decides to override a religious group's objection to medical care only this time with a clear-cut distinction of the doctor being a flat-out murderer while B5's doctor made a decision with tragic results but it was a decision that most of us would also have made. (And I suppose some people might argue that this wasn't deliberately a remake but really religious refusal to accept medical care is so extremely rare that it's far more likely the BSG writers got the idea from B5 than it is they got it from real life.)
But the ending was jaw-dropping. Two angels standing in the middle of our (mine, yours) modern-day NYC discussing God's plans while viewers are treated to supposedly threatening but actually quite innocuous images of robots? Seriously - angels? Toy robots? And Kara turning out to be a ghost more or less? Which also makes that undamaged ship she flew back at the start of season four a ghost ship despite having a physical existence. God apparently programmed the co-ordinates into the ship. (I really wish I was kidding about all this.)
Even without that we're treated to the spectacle of the last remaining humans (oh wait, there are some already on the planet - again God's plan) deciding to destroy all their technology on the idea that this can "break the cycle of violence". How not having tools and shelter will do that - even not having weapons - is quite unclear. Having fertile soil and lots of game doesn't guarantee survival - just look at the history of settlers in the Americas and the BSG people are deliberately going to technology centuries earlier than that. And spreading the remaining 38K people around the planet? There has to be some population density for a birth rate high enough for the group to expand though I suppose there's always those tribespeople wandering around. I understand why Chief might want to go live alone but why does Adama? The show writers messed around for a couple of seasons then had to rush everything.
Really it was too much to expect the show to end well. Season four continued most of the fantasy elements from the previous season but added quite clumsy storytelling, the kind of mistakes that usually only happen with beginners. For instance, one episode about two-thirds through devotes almost half its time to one of the most shameless exposition dumps I've ever seen. Two characters, one who has regained his memory and the other returned from...well let's just say she also regained her memory, those two characters give monologues of backstory so we know how the Final Five and the Cylons came to be. That's right, it sounds like they're reading out of the show bible for twenty minutes. It still doesn't make any sense. (Why does everybody call them the Final Five? They're really only final from our position as viewers.) And then there's the episode where Kara talks with a piano player for an entire episode and who, gasp, turns out to be imaginary though most viewers will have much earlier figured this out. Or the kind of fake lesson that mortality makes us human - the kind of dumb stuff the original Star Trek pushed but that we could easily ignore then because it's only a minute or two instead of BSG agonizing over it for hours. It's false because mortality has no more bearing on us being human than our chemistry being carbon-based - we can't change it and in any case share this with pretty much every other living creature.
Or filling the final two episodes with completely pointless flashbacks - the only remotely logical reason I can see for these is that the BSG writers thought this was "character development". Folks, you're about to end the entire show - if the characters aren't developed or revealed or explored or expanded by now then none of this helps. We already know that Lee and Kara were attracted to each other, that Gaius claimed to love Blondie (I have no idea what we're supposed to call her), that Ellen and Saul actually do love each other and so forth. If anything Admiral Adama needed this focus since he had become the fuzziest, most pooorly planned of the major characters. I'm far more intrigued by the revelation that their culture had strip clubs but then BSG was a show that avoided being science fiction as much as possible. "Keep It Familiar" must have been posted on the writer's office walls. Much of the final episodes revolve around the importance of Hera but clearly everything would have worked out the same even if she had died.
Which is the other oddity about BSG. As the show went along there's so much discussion about the Cylons being machines but there's not much that marks them as machines. Apparently they're medically identical to humans and display no superior intelligence or physical abilities. So what makes them machines? Is this the point that they eventually become human?
Not many (or actually any as far as I can find) people commented about how authoritarian the show became. The mutiny was easily the highlight of season four, the kind of clear storytelling the show had earlier where people get caught up in events and sometimes make wrong decisions. And it's built on the entirely reasonable resistance to working with Cylons that you would expect from people who watched them nearly wipe out all of humanity. But once the mutiny is down then the Admiral and President get to make the decisions, no more democracy. Not that we saw much democracy earlier but maybe this was the point of that half-baked section The Razor that told us sometimes leaders have to make hard decisions and we're expected to follow orders. (The Razor lost most of its point by having the captain explain herself - I guess so that we don't think she's insane - and by having the lead character ask for redemption at the end instead of owning up to her actions.) This authoritarian bent is also why the President increasingly sides with the military until it seems like there's no real distinction, in sharp contrast to the show's first season which was built around the conflict between military and civilian authority. But hey that must all be God's plan as well.