First, here are the thoughts (comments) I left there:
I think that Moore is in a way stuck with the clock running out. It’s kind of like the X Files situation, where there’s this complicated Smoking Man story running in parallel with episodes that are just entertainment. Some fans are coming for the long story, some for the short story. As the show nears the end, the pressures of wrapping up the long story, of answering questions, can overwhelm the per-episode storytelling. And the unfortunate thing is that usually mysteries are more interesting than their solutions. That being said, I was surprised to see the storyline take a turn to Yet Another mutiny, plus Much Ado about babies.
@Darren I’m trying to track the major unresolved issues in my Zak Adama is a Cylon blog. (And the BSG wiki and other fan sites are probably doing so as well.)
As I said, I think Moore is in the same place as any successful “first big idea” show - like Lost, Heroes, X Files, and others, the explanations are a lot less entertaining than the mysteries themselves. Particularly in a highly-constrained format like BSG, where you’re basically doing a four-season long submarine drama, your only choice is to mix and match all the existing players in every different way you can think of.
I thought the miniseries and the first season were extraordinarily strong, but I don’t know if it would have been possible to sustain that level of drama, tension and mystery while also moving towards resolving the show and all of its plot points.
I think you need to consider the idea of the long story, the story arc. As I said, most of the "One Big Idea" shows have had trouble sustaining once they had to start answering mysteries:
The only time I have seen it done really well, the entire multi-season arc of the show was planned out in advance, in Babylon 5. Since they knew from the beginning what plot points they needed to hit, they were able to do arcs that ran across years, with someone saying something that would connect to an episode that happened several years later.
You also have to recognize that most shows have some constraints of cast - if you've got half the cast who are good guys, and half who are bad, you can't lose too many from either side. This is a common situation in all drama - if you have a really compelling good guy, and a really compelling bad guy, all you can do is situations in which one or the other almost prevails... but both survive. BSG initially turns this a bit on its head as the humans are clearly the losers, but you can see in the original BSG what it could have turned into - in each episode Baltar almost gets the humans, or the humans almost get Baltar, but nothing ever actually changes.
Moore is playing out about as much of his canvas as he can, without changing the major players: BSG fleeing, then an occupation that reminded of Vichy France or Iraq, then more fleeing, then an alliance with former enemies. The only thing he has left is resolving mysteries, including some final unification.
BSG asks a couple big questions: what do you do when you lose, and what do you do when you win? These are fundamental questions of war and peace. Because of our terrorism preoccupation, we related them mostly to Iraq, but I think you'd get more out by considering the situation in Israel. When you fight each other, year after year after year, how can you ever sit with your opponents and reach a peace? What happens to all the people who dedicated their lives to fighting, when a truce is declared?
Moore's position om these issues are fairly clear - politics is painful, but it's the only way out. It's a striking repudiation of the Bush-Cheney "power comes out of the barrel of a gun" philosophy. By any conventional measure, the Cylons won a stunning "shock and awe" victory. All should be contentment for the Cylons now, right? Moore brilliantly recognizes that we're in a world of 4th Generation Warfare, where the old assumptions no longer operate - tiny bands of insurgents can make life hell for the "winners" - the war never ends, while a single member of the enemy lives. As well, he recognizes that winning, on such a scale, with such destruction, could tear a society apart as it faces the regrets and recriminations due to its actions. And so the Cylons, having achieved a great victory, find that their worst enemy is themselves.
The BSG miniseries and first season (and for that matter most first seasons of "ideas" shows) are compelling because it's all new - the world, the characters, the issues, and the mysteries. It was particularly well constructed to connect to the terrorism fears of the day. It was always going to be hard to sustain that. I think they did ok in the second season. New Caprica I hated. The endless talking at the trial I hated. Whenever they made their connections to real-world events too obvious, I disliked it. When you compare with all the time-travelling incomprehensibleness that the Lost and Heroes writers are using, Moore is actually taking us in a fairly straightforward way to the end, with some entertainment along the way.
So I don't think Moore has run out of ideas. I do think he's running low on plot points to hit as he wraps up the mysteries. Solutions to mysteries are almost always less satisfying than the mysteries themselves. And I do think it's maybe hard for Canadians to identify fully with this idea of enemies coming to a peace, but the mutiny plot actually works on many levels - whether it's the US Civil Cold War, where Obama is trying (without much obvious success) to bridge the gap between Democrats and Republicans, or it's the situation in Israel, where it's clear the only solution is for two peoples who have been fighting for decades to come to a peace agreement - peace is hard and complicated and messy, and often people aren't as enthusiastic about peace as one would like.