Not that the finale wasn't intuitively written. Which is the second issue, because while it's a fine story, it turns against the preceding flow of the narrative in some pretty stark ways that, assembled, seem pretty revealing.
Let's start with Tory, not because I love her so much or anything, because what is there to love beyond the gifted Rekha Sharma? Not a lot. She was the mystery ingredient in the Final Four, the "most exciting" open-ended character, who in the end got the least interesting, most cardboard-villainous story of all. Thinking back to the balance of the Final Five, above, let's think about her for a second. Tory Foster is not Slytherin, she's Ravenclaw -- Ellen's Slytherin -- Tory is Air, Mind, the Invisible Girl, Thinking, taunted and haunted by dark emotions she can't see directly or ever explain, shooting out dark roots into Intuition and Sensation in order to stabilize herself against these shadow emotions and fears. (Compare Buffy's Willow Rosenberg, for an easy example.) The Final Five have lost their Thinker; it's no surprise that soon after, they give up even the touchstone of transcendence, shooting Sam into the sun as an artifact of technology, and become the Final Three.
What's troubling is that these Final Three, eventually, will agree that this is okay, even appropriate. Laudable, even. The show claps Galen on the back for severing the group's ties with the infinite, breaking a peace accord through murder, and eventually damning all but three Cylon models to death. Which, whatever, that's fine.
Only at the same time, Lee is warning us about our science outstripping our souls. Just after sending Simon the doctor and Cavil the atheist genius into a black hole, and a little while before the Smartest Man in the Twelve Colonies decides to become a farmer. Because courage, not intelligence, is what earns you love, and the right to exist. And right about this time the Fleet is giving up all intellectual progress they've ever made, and lying down in the grass and praising themselves for it, because technology and intellect and progress and mental strength are not "the best part of ourselves," any more than Tory Foster deserved to live. Human progress is typified in the glorious decadence of Caprica City, where if they're not fucking they're puking on themselves: "Commercialism, decadence, technology run amok" are inscribed as natural human endpoints, and the Hybrid and Lee agree, at different points, that cities and civilization are the root cause of all evil. And even though I personally found the characters' resolutions -- yes, including Kara's, and the angels' -- completely satisfying, that can go on the list too. The story steps up to the brink spiritually on at least three fronts, and then tosses up its hands, saying those lynchpins of the series no longer signify. Not for the lack of answers, but for suggesting that the questions themselves aren't worth asking.