I haven't had a lot of problems with the personal story lines, but the editing of the last episode set my teeth on edge. Usually this quick back-and-forth between scenes technique is done to emphasis parallels between ongoing situations, such as the excellent use of this technique during the Pegasus episode where Cain and Adama finished each other's sentences as they plotted one another's assassination. But the Baltar interrogation and the love quadrangle simply didn't have enough thematic elements in common to warrant the use of the inter-cutting. It failed to heighten the tension for the Apollo/Starbuck scenes, and it actually undercut the drama in the Baltar scenes.
That said, Apollo ordering his wife into danger to save his lover? Excellent. Helio shooting Athena at her insistence so she could rez on the basestar? Excellent. Tigh, Baltar, Caprica and even D'anna's character journeys this season have been great. I strongly disagree with the idea that the show can no longer be supported by "character driven stories" on the basis of a few below average scenes from a couple of episodes.