While I understand that Ron Moore was going more for a character-based drama, significant breaches of continuity like the whole Tomb of Athena star map being ignored (the whole point of the huge Season 1/Season 2 cliffhanger) detracted from the show as a whole.
I understand he didn't want to emphasize plot as much, but at least being consistent with it would have gone a long way. Personally, when I realized the show was being picked up for a second season, and was becoming a smash hit I would have sat down, figured out in at least some detail what the Cylon plan was, what the real deal was with Earth, and at least a vague sketch of the overall direction of the show. As it was, it seemed like they were just pulling new stuff out every few episodes trying to top it for how awful they can make life for the Colonials.
As for how religious the finale and last episodes were. . .
Yes, religion was part of the show from the beginning, but it was very ambiguous which (if any) of the religions was right.
Roslin's visions could have been prophetic, or they could have been drug-induced. Baltar's vision of Six could have been his own mental breakdown at guilt for causing the collapse of civilization, or it could have been Cylon biotech implants, or it could have been an angel. Baltar's knowing the right place to attack on the tylium refinery could have been divine guidance, pure dumb luck, or a brilliant flash of insight. The prophecies about Kobol that came true could have been prophetic, or they could have been just vague enough that almost anything that happened there would count as filling them. When Starbuck came back, we were left wondering what happened. Was she a Cylon created clone, created from DNA taken while she was held captive, placed in a Cylon-manufactured Viper? Was she somehow sent by God/the Gods? Had some weird Star Trek-esque space anomaly thrown her through space and time to meet with the fleet later and it only looked like she'd exploded?
Up until the last minutes of the finale, every single religious thing that happened in the show could have been explained as a coincidence or with science and technology. Then "Surprise, it was God after all, and the Cylon religion was right!" didn't feel like as much of an answer as a cop out.