Dollar for dollar, I [still] feel the original Mercenary's Handbook (FASA 1616--available officially as a PDF still) has the best campaign system for the BTU. Mendrugo got it in one. It is able to track multi-regimental operations--and develop the opposition from a broad stroke down to individual elements or squads as desired--and still keep track if your character got wounded off-screen (again, as you desire). But there is room for some slight, almost idiosyncratic, tweaks, that is true as well.
But yes, as Daryk says, CO is the go-to nowadays.