It's been nearly a year since the end of the third season, and after such a long wait, it shouldn't be surprising that the audience would have high expectations. In fact, those expectations were nothing but heightened after the taste provided by "Razor" in November. It's practically a given that this episode failed to meet those lofty desires, but that may prove to be a good thing.
For some, the third season finale was all about throwing everything and anything against the wall, seeing the patterns that formed when it congealed, and using that as the roadmap to the series' conclusion. On the other hand, it also felt like a finale that was meant to shock the system, reinvigorating it towards the goal of a more frantic finish.
Three major items dominate this episode, all of them focusing on matters of faith. The Baltar situation is the most straightforward. Baltar finds himself among a small group of monotheists who consider him to be a prophet, even a savior. The fact that they are mostly young, attractive women does not escape his notice, and does take advantage of his new opportunities. Yet very quickly, his perspective turns more serious.
Baltar is brought a young child with a deadly illness, in the hopes that his prayers might save him. This leads him to a rare moment of honest self-reflection. He admits his own failing, his own weaknesses, and offers himself in place of the boy. It's not something that Baltar would have done in the beginning of the series. Shortly thereafter, during an attempt on his life, he is ready and willing to die in payment for his sins. Part of that is self-pity and guilt, but it does make one wonder if Baltar might become someone worthy of the adoration his harem provides. (Though I could easily see his most violent protector becoming a problem before much longer.)
Second, we have the situation with the four newly revealed Cylons. All of them are in a position of trust within the fleet, and in the face of Kara's return, none of them are suspected. Ironically, Anders effectively saves the fleet when a Raider seems to scan and recognize him. (This brings up an interesting point; are the more "primitive" Raiders more aware of the hidden Five than the humaniform models?). Tigh and Tyrol both reaffirm their own humanity on a constant basis, even as they all fear taking action against their apparent WILL.
What makes this interesting is the callback to the first season, when Boomer was caught between suspicions about her true nature, her programming, and her humanity. Not only does the audience know that she failed to overcome that programming, but we've seen Athena successfully chart her own course (at least, it appears to be so). Now we have the same situation but amplified by a factor of four, and with a more profound effect on the Cylons themselves.
The third and final aspect is directly related to Kara Thrace and her return from apparent death. Clearly she wants Adama to believe in her, but pragmatism is getting in the way. Also, the circumstances of her return are questionable at best, and given justified fleet paranoia, grounds for exactly the treatment she's given. In her nearly-religious assurance, she's completely dismissing everyone else's perspective.
Which is not to say that she's wrong, because it's far more interesting if she's absolutely right. Kara's bloodhound psychic alarms are remarkably similar to Roslin's reaction upon the fleet's arrival in the Ionian Nebula. Roslin's reaction was preceded by visions shared with Caprica Six. One could speculate that the "activation" of the four of the Final Five at the exact same time was a meaningful correlation.
In my comments for "Razor", I noted that the prophesies regarding Kara Thrace and her role in the destruction of Humanity may have been easily misinterpreted. What if Kara is meant to bring about the end of both the Human and Cylon races as they are, by bringing them together based on a common legacy? After all, in "Eye of Jupiter" and "Rapture", the Temple of Five was built by Humans over 4000 years earlier.
One theory I've had for some time is that every "cycle" of the story begins with Human and Cylon separate and at war, and ends with the two races merging into one species. They recover to the point of sending out colonists. The colonists struggle to find their own identity while the "originals" continue to evolve. The colonists are seeded with the genetic material necessary to survive the next cycle, while the "originals" help both of their "children" to find their way.
So by this theory, the Final Five are not constructed Cylons in the sense of the seven humaniform models, but rather, genetic Cylons: Humans embedded with ancient Cylon DNA. Tigh, Tyrol, Anders, and Tori would not have false memories of their lives because they truly lived them. They are Human, but a part of them is also Cylon.
Also by this theory, Kara would have been saved by the previous cycle's "humans", those now on Earth, so she could lead the fleet home. They would have been able to give her a new Viper and the sense of where to lead the fleet. It's possible that Roslin is equally "attuned" because of her use of the kamalla drug. On the other side of the equation, the Cylons may also be following such instructions through the guidance of the "hybrids" and Cylons like D'Anna and Caprica Six.
Of course, all of that speculation may be wrong, and that is the allure of the final season. This is the season where the answers should finally be forthcoming (albeit in chunks, thanks to the writers' strike and Sci-Fi Channel scheduling), and there will certainly be unexpected twists and turns. However, I do feel that the foundation has been laid in the previous seasons, and it all comes down to a matter of context. This episode is just the first step in that process.