Great first half, slow second half IMHO.
It really lacked number three. Why couldn't she make an appearance? Why wasn't she involved with the story?
I think the rationale is that this story focused on the original plan -- Cavil's plan. It's the one that lead to the annihilation of the colonies and started everything.
His plan was supposed to have ended as soon as it began. Everything that occurred after the nuking of the colonies was improvised (as he made abundantly clear) and every day that passed, his plan became more and more convoluted. By the time this movie ends, he finally surrenders and gives up on his original plan and begins concocting a new one beginning with the boxing of his own model which, in his eyes, are completely corrupt and beyond redemption.
That said, Three's story was completely independent of Cavil's. It wasn't a part of "The Plan" at all, but a repercussion of "The Plan" failing. So while it may have been one of the things I wanted to know more about, none of that was directly relevant to what this story was trying to explain.
It's also why the series seemed to be so aimless for a good stretch of its run. Because it effectively was
. Cavil was forced to make it up as he went -- he hadn't planned on a contingency for the initial genocidal assault to fail and the first half of the series was him trying to bring his plan back on course.