According to the podcast, this was a last-minute desperation decision to try to breathe some life into an episode nobody was happy with. They felt it started slow and unfocused, and by flashing forward to the climax they hoped to inject tension into the first few scenes: who’s that, why’s Apollo pointing a gun at him, etc. Pretty much a Hail Mary device, according to RDM, and not the way the ep was originally planned.
The negative thrust of the podcast, and the basis of RDM’s criticism, is basically three-pronged. First, he thinks the Bill Duke character belongs in another show; he’s too evil, too simplistic a bad guy, whereas this show likes to traffic in shades of gray. Second, he thinks Apollo’s journey is too linear; he asks Zarek up front for a lead instead of doing his own investigation, he goes right to the source of the crime with no detours or dead ends, he zeroes right in on his target, boom-boom-boom, without any twists or turns or surprises. He says they were going for a Heart of Darkness feel, sending Apollo into a labyrinth of corruption, except that the maze turns out not to have any branches. Third, he thinks they missed the mark badly on the economic/philosophical foundation of the story. There’s an interesting debate about the degree to which an illicit economy should be allowed to operate, how much it serves a society, and whether Roslin’s desire to stamp it out makes practical sense, but an economic argument doesn’t make particularly good drama, so they shied away from it and threw in the child molestation cliche to make it visceral to the audience. Take those three things together, and as c’plant says, it makes the show feel to RDM like “regular TV” instead of great TV.
(Oh, and there was a plot point that RDM regrets cutting: Apollo’s flight on the raptor to Prometheus is his first time in the pilot’s seat since his spacewalk, and he’s apparently close to the edge of failing to keep himself together. Pretty important stuff.)
I’ll give him the third criticism, but on the first and the second, while I agree that they didn’t accomplish their intended objective, they landed on something else equally valid, and RDM is either blind to it or he’s deliberately selling himself short to buy some audience sympathy, as noted above.
On the first, I don’t mind a clear, unambiguous villain. This is a dark show, reflecting the darkness of reality, and it’s certainly true that there are some very, very bad people in the world, people for whom killin’ is too good. The show doesn’t need to paint every single person as a conflicted mix of motives, because that’s simply not how the world is. Every now and then, we’re going to run into somebody who is just plain rotten to the core.
And taking the second, in combination with the first, we actually have a totally different journey for Apollo than what was intended, but one that’s equally valid and, in my opinion, even more enlightening as to his character than what they were going for. By putting the flashforward at the beginning, by announcing that Apollo is going to wind up toe to toe with the villain, they basically lay out the arc of the story in advance. Then, maybe a third into it (or so; I forget the exact structure), we meet that bad guy, in the scene where the hooker and her daughter are taken, and we see that he is, indeed, unredeemable. At the end, Apollo will be staring down his sidearm at a man who deserves to die.
At this point, we don’t need twists and turns. The point of the show becomes getting to that final confrontation, and seeing what Apollo decides to do. We know, from a practical point of view, that Apollo is basically going to have no choice but to shoot the guy. And yet, that’s not what we expect from him and his Boy Scout outlook. He’s going to pursue the investigation, he’s going to follow his leads and find his target, because that’s his duty. But because of the opening flashforward, we know he’s marching straight into a no-win situation, because Apollo is not a murderer. It’s not simply a suicidal impulse, because his point about having been tracked is a good one; if anything happens to him Galactica is going to take a large-caliber shit right on Prometheus’s face. Even so, we get the sense that he doesn’t actually care, that in some ways he hopes that’s exactly what happens; there is, indeed, a suicidal undercurrent to his quest. But when he comes face to face with such an unapologetic monster, he’s actually coming face to face with his self-torment when making impossible moral choices. He throws himself carelessly to the wolves, and it isn’t until he actually pulls the trigger that he makes a choice not just about living or dying, but about who he is willing to be in order to survive.
So it’s not Heart of Darkness. It’s Lethal Weapon. 
All of that being said, the ineptitude of the prostitute’s climactic speech comes perilously close to blowing apart the entire show. We don’t care about her. We care about Apollo. We care about his feelings, not hers; we care about his self-image, not his life with this woman. For her to blather on and on, “I’m not her, that’s what this is about,” cliche after cliche, deflates all the emotional value of what’s been happening to that point. It should have been a simple, cold, flat moment, short and cutting. Something like:
Hooker: “I’m not coming.”
Apollo: “What? …I won’t turn my back on you.”
Hooker: “You turned your back on her.”
And she’s gone, leaving him alone with his history. That’s all they needed. The elaborate flashbacks, the lengthy monologue, all totally unnecessary, and indeed counterproductive. And the episode is significantly weaker because they blew the climax.
Mask that poor finish, though, and imagine a better scene in its place, and you can see how the remainder of the episode suddenly gets a lot stronger.
So that’s what I’m focusing on.
Not their finest hour, by far. Possibly even their least successful episode, though I think “Final Cut” still qualifies, and as others have said even mediocre Galactica is still more enjoyable than just about anything else on television.
And I’m definitely looking forward to next week.