I disagree, the mystical aspect of the show has always been interesting and exciting. The inherent drama of Adama's call to find Earth coupled with his actual ambivalence about the whole endeavour was great. The military episodes also had the most drama, because we got to see characters evolve under stress. I'd say the Kobol episodes were the strongest, and they contained not only troops fighting a pitched battle against the Centurions, but also the wonderful scene where Adama drowns Hera in an almost biblical gesture. This scene, of course, turns out to be one of Baltar's fevered dreams, but then the camera pulls back and we find he's in a bone field. Something horrible has clearly happened on Kobol, but we never find out just what.
Also, Scar was a fantastic episode and it gave away the line that the Cylons are, at least in some way, emotionally scarred by their deaths. This dropped hint has become increasingly relevant and this was an episode cribbed from any show or movie about fighter pilots.
My thesis is, the episodes that focus on mysticism for mysticism's sake are never as good as the episodes that allow the mysticism to organically seep into the conflicts and drama that surround the rest of the show. The writer's focus on the day-to-day drama of the fleet, including combat and survival, hones their viewpoint and makes for better episodes.
I think BSG's treatment of mysticism has changed a lot since the beginning. I was mainly interested in it at first because of two things:
1) Baltar and his "guardian angel" exemplified the rational mind being pushed beyond the limits of the rational. His dilemma was not only "science versus spirit," but "who does a skeptic turn to for comfort, meaning, and in his case, absolution?" These questions were core to the theme of the show at the time, which had everyone looking for a way to explain their traumatic situation.
2) They pointed to a "plan," or a "greater unknown" that in story is one of the most tantalizing devices ever. I wanted to be frightened and awed of the cylons because it upped the stakes: it wasn't just survival that was at stake for humanity, but they had to discover their role in this supernatural plan in order to restore the balance that they forfeited when they created the cylons in the first place.
The Kobol episodes that launched season 2 are where I thought things started going wrong, at least for this gestalt of the show. The tantalizing promise of Baltar reaching the opera house (which at the time was Kobol) was subjected to prevarication like Baltar having to prove himself a man before Six and the map to Earth, which might as well not have existed for all the good it did.
At that point, I feel the thematic locus of mysticism was left behind. Naturally, the mystical issues couldn't have climaxed at that point without answering the questions that defined the show, so religion and mysticism became mere devices to grab interest. "Prophecy" was stacked up to build suspense for later in the season under the unspoken promise that it would pay off thematically, but in practice it just delayed our expectations, and in the end, deferred explanation to the next season, and again the next. At some point, I would actually say at "Scar," the writers began trying to rationalize the irrational.
Let's not forget that at one point the cylons were themselves a "mystical force." They were rarely granted POV; they were a force of nature. Giving the raiders pathos in "Scar" was the first attempt to try and explain them. Then we jumped into their basestar for a look-see, and all the trivia surrounding the final five, cylon society, the civil war, blah blah got churned up. Not necessarily in that order. My point is that mysticism is feeding on itself, raising technical questions with technical answers like, "what are Starbuck's visions?" "what is the role of the final five?" "who is the fifth?" "why are they revered?" etc. What they are not doing is posing meaningful thematic questions that deal with their characters' situations, like they once did. The one exception to this I can think of was Espenson's first episode this season, which was about Baltar's experience of religion, and why he needed it at that point in his life.
God (heh), I'm sorry about all the text. I've got another long one coming up on the subject of last night's episode, if you're interested.