If we go with the West Matches concept, I think one way to control the "level"of the enemies is by having quests/missions/zones of varying hostility, perhaps labeled by the value to the enemy organisations. Undertake a mission to plant a bug in an outlying outpost, and you'll go up against gaggles of rookie zakos. The intel from that mission could unlock a secret military facility that needs destroying, which would have the usual zako backed up by a murder of more experienced ones. We could also indicate boss zakos as special assassination missions too!