I'm not sure how/when it is appropriate to bring in some of the villains.
Splitting up enemy groups has worked really well for us- we've only done it with more obvious ones so far (like the tamahawk gatormen).
The bosses and more elite units seem trickier to me- I'm not totally sure how best to incorporate them.
Part of me thinks it would be interesting to replace whole groups with a boss baddie or two (he'd just activate a lot extra).
Someone on one of the forums had a great idea of placing a unit's boss at the back of their reserves. Once all enemies from the reserves had been killed, the boss would spawn next. I haven't played it that way yet but really liked the idea. It keeps it very simple aside from tracking the enemies in the reserve, which can easily be done by placing them behind the boss once they have been removed from the board. The boss would activate just like a normal unit of that type with the exception that they are both colors (sneaky job PP), very similar to the Boss rules for KS exclusive chapter 2.5.