BSG was completely badass and I really didn't mind the ending. I think the writers strike made it worse than it would have been, because they had time to over-think things. I'm reminded of the South Park special where they show how they make each show in just 7 days. They have pretty solid evidence that not over-thinking their episodes results in a better final product than if they tried to make every SP episode "perfect".
That said, BSG did NOT end with gaping plot holes. They sewed everything up pretty dang neatly. The least believable part is that people would leave so much technology behind. I can understand sending the ships into the sun, but I interpreted it as them going back to nature, and probably starving en masse as a consequence of not keeping high quality metal fabrication, tools, guns, etc around. Its a minor issue, I mean how are else are they going to explain the fact that we in fact have not found unexpectedly advanced artifacts 150,000 years old? They were kind of forced to go this route considering they had to explain the importance of Hera, which was to make her Mitochondrial Eve.
Yes, Seasons 1 through the fourth or fifth episode of Season 3 were better than the majority of what came after. So what? Even the worst episode of BSG was many times better anything else on TV at the time. I don't understand the complaining about it. The writer's strike screwed them, nothing they could do, it was still the best damn space show period.