Last time I played Empire, I added the Skirmishers to the Flagellants. Mainly to give the flagellants a bit more staying power - as they are hard hitting, but die quickly. As they must follow up the Flagellants tend to get chewed up pretty quickly, but the skirmishers let them soak up more damage. Also the 25pts seems more worthwhile when compared to 1/3 of a flagellant unit, rather than halberdiers.
I also wonder if by putting the skirmisher stand at the back, facing backwards, it gives you nearly 360 vision, handy for clearing out pesky flyers that land behind your line!
I have tried them with the halberdiers - this time at the front to give the +1 attack - it sort of works, but they are still pretty weak.