While information about Skirmishes System are still coming, Zombie Columbus has unveiled most of details in the latest Developer Diary: SoM Skirmishes: Overview.
Skirmishes are short, accessible, randomized, scalable, story instances with incremental rewards. Why Skirmishes became this can best be explained by discussing what the designer's goals for the system are. Everything we added to Skirmishes was done with a high level "vision" in mind.