I always thought that the they were trying to squeeze too much into The Peacekeeper Wars; more than could possible be done in two extended episodes. I listened a commentary on it, and the creators said exactly the same thing. Before they were cancelled, they had this whole season planned about everything that was going to happen; when they discovered they were cancelled, they tried to make a movie out of it, but that wasn't possible, so it got trunkated into a mini-series. It shows.
They did an excellent shop with the amount of on screen time they had available, but it wasn't enough. They were trying to tell a whole season in two episodes. I would have liked a sixth season over a movie, but a movie over a mini-series.