I loved, positively loved, the first two seasons of Galactica. Third season was mostly okay, but it started to go downhill, I kept watching until the finale. . .and had a huge "WTF" on my face at the end.
1. It's a ridiculously huge strain on disbelief that tens of thousands of people, from a spacefaring (and according to Caprica, post-cyberpunk) society would all willingly give up technology and revert to a stone age population. They didn't have people who said "heck no" and wanted to stay on their ships or land them? Just because Apollo said he didn't want a city everyone went along with it?
They could have at least set up a city on some island, called it "Atlantis" and salvaged a tiny shred of credibility there, saying that some went to live with the natives, others built a city of Colonial technology on a lush island.
2. The entire Tomb of Athena plotline on Kobol made no connection. The entire cliffhanger between the first and second seasons was based on the fact there's a star map on Kobol leading to Earth, our Earth (as in the stars in the sky are the same). The only way that works is if the original residents had been to, or come from Earth. The "Earth" they find that's a nuked wasteland and wasn't our Earth threw that out of the water, and the idea that our Earth was apparently uncontacted? Huge continuity problem with the map from Kobol.
3. The religion stuff was always subtle the entire time, a sort of "is it/isn't it". It was always ambiguous up until the end if Baltar was just having delusions based on his guilt, or if there was some piece of Cylon biotech in his brain producing the image, or if Head Six really was an angel. Everything religious could have been a coincidence.
Then the resurrection of Starbuck dumped on that one, and if that wasn't enough, the end with the angels walking in modern day Earth talking about everything that happened just fell flat.
4. It's a little of what TV Tropes called "The Chris Carter Effect", for X-Files having the same thing happen to it. They imply early on that there's masterful plotting and a huge overarching plotline, but they haven't really given it any thought, then when the show actually becomes a long-running hit they realize they have to start to show that plot and are winging it and it really shows. The longer the show went, the more clear it was that they really didn't have a long term plan. The Final Five, the "Earth" that wasn't Earth, the Cylon prophecy about not following Starbuck, all felt the were pulled out of nowhere and shoehorned in or dropped. They even admitted the whole reason for the lost "Daniel" Cylon was they made a mistake in numbering the models and had to account for why one was missing. Big part of the Cylon origin story was a patch for a writing mistake when they realized the fans would notice that sort of thing.
5. Too grimdark. Yeah, this was a darker and more realistic retelling of Galactica than the campy 70's version, but the earlier seasons always had moments of hope. Somewhere around the 4th season they just started to pile on more and more bad things, make things darker, more grim, more bleak, without respite. They were practically losing more characters to suicide than enemy action at one point.
6. "No aliens" An original key conceit of the show from the writers was that there were no alien life, that intelligent life arising would be so incredibly unlikely that they would never see another sentient race, ever. Edward James Olmos even said he'd walk off the set if they ever encountered aliens. So, having them encounter humans that were genetically identical to them that apparently evolved separately was countless times even more unlikely than some random alien race. There was a brief hand wave about divine providence, but for a show that had previously couched divine actions in plausible coincidences, this was just way, way too far.