From a reader:

Great column in commentary.
Moore clearly had a season long story arc plotted out when BSG started. The first twenty 26 or so episodes are fantastic and have a great sense of continuity. Moore molds the Human/Cylon mythology into something interesting and mysterious. Those episodes do a great job portraying the urgency with which the humans are fighting for their lives. The series did a excellent job at reminding us that despite all of our flaws, there is evil in the world worth fighting.
Cracks in the series start to appear in episode 27-28 (The rather boring Black Market and Scar episodes), and the wheels really start to come off in the Cylon-centric Downloaded episode in which the Cylons begin to ditch their plans at annihilation. At that point, Moore had spent over 30 hours building up Cylon mythology/allegory and then proceeds to tear it down, sowing the seeds for the helter-skelter third and fourth seasons.
I think if Moore had a multi-season road map at the beginning of the series it wouldn’t have gotten so bad, so quickly. The moment they had to start “making it up” things quickly got out of control and the series lost focus of the big picture. They had to pile deus ex machina upon deus ex machina to move the series along.
Of course, this isn’t unique to BSG- see Mad Men, Sopranos, Friday Night Lights. Creative creep isn’t a new thing, but its particularly frustrating when it happens to good serial television.