As with part one, the empahsis on the "extremist" fringes was not helpful. On various occasions throughout both parts, Dawkins suggested that such people sat on an unborken spectrum with more moderate believers, perhaps even constituted the logical endpoint of faith. I don't think he really managed to prove that though.
I thought the last twenty-or-so minutes were by far the strongest. The discussion with Richard Harries was interesting and much more relevant given that such people are the kind of believers we are most likely to meet (at least I hope that's the case). I really liked the bits about the immanence of morality as a counterpoint to the religious idea that it needs to be imposed externally. It's an idea which I think is potentially very liberating.
I still think the show was a missed opportunity. There's a seemingly endless stream of shows extolling the virtues of faith, but very little putting the case for atheism. Indeed, I can't think of a comparable show in recent times. I doubt it's won atheism many new converts. Pity.