I admit, I haven't watched BSG on a regular basis since about the third season. I just lost my taste for the show. It really does seem like the writers have jettisoned any sense of plot or theme or character development for the sake of being brutal and topical. I too find myself scratching my head about the Cylon "plan." They WERE supposed to have a plan, right?
It's also the politics of the show that weigh heavily upon my bleeding heart. I've long been troubled by the thought that BSG is basically a fantasy extrapolation of post-9/11 American society, but told from an ultra-conservative mindset. Consider: the Cylons are religious fanatics operating without any real plan beyond "kill the unbelievers." There's no point in trying to see their point of view or come to a peaceful settlement, because they HAVE NO POINT OF VIEW. Not even THEY are clear on their own agenda. The human leader is a divinely-appointed savior who is literally in bed with the military. Anyone who disagrees politically is either a collaborator, a moron, or just pushing their own personal agenda. Characters who could be seen as truly heroic (Gaeta, Helo, Lampkin) are punished for it as the plot moves along, and borderline psychos and just plain incompetents (Apollo, Starbuck, Tigh) are elevated to grand status. Tom Zarek, even though he's technically a villain, was originally made out to seem like he might have a legitimate political beef with the Colonial government, but eventually he's just revealed as another self-promoting schemer. Gaius Baltar goes from Bill Clinton to Saddam Hussein to...whatever he's supposed to be now in way too short a time, assuming whatever role the writers needed him to assume that week. It's frustrating, and I think the ending will be equally frustrating.
That being said, I kind of liked the Bob Dylan references. I've often thought that maybe great artists had some conduit to the Divine, and it's an interesting concept to think that, in some far flung corner of the galaxy, there was a poet or songwriter tapped into the same conduit as Dylan was. And the song does fit with the overall mood of the show.