Our game group has played quite a few games and decided about a month ago to take the Pegasus board out for a while to make it harder on humans, and then this last weekend decided to mix things up by adding in the Cylon Fleet board and re-adding Pegasus. We always play with the skill/destination/crisis cards from Pegasus and Exodus, but have (of course) kept the CAG cards out when not using Cylon fleet.
Our experience was an epic fail, and it sort of shocked us. It was the first game ever, I believe, that we actually stopped playing in the middle of a game, and at only 2 distance of movement at that, and said "I hate this, let's stop," and we all agree to it, and we were so disenchanted that we put the game away to do something else for a while.
Getting to the 2 distance was a long slog. In part, this happened because the Cylon was discovered on the first turn. It was Cally, and she shot me (Gaeta), and then we successfully airlocked her afterward. She left the Resurrection Ship and went to the Cylon fleet, then began making the jump track go down and made us put out civvies or raiders repeatedly. So thus began and continued a pattern for the rest of the game until we gave it all up. We put out ships, then we moved them around and escorted them back; we put out cylon ships and then shot cylon ships, then more ships were put out and more cylon ships were shot down. I came back from the dead as Dee and I was given repeated XO to communicate civilians or command vipers. I rarely left those two spots. Someone else (Zarek) shot from Pegasus. A pilot (Apollo) was in space cleaning up whatever remained. This was all the game became. It simply got to be tedious.
I recognize that not every game would go this way: the cylon did not have to reveal that early and did not have to use Cylon Fleet all the time. But I guess I'm asking people generally: Do Cylon fleet games generally go better than this?