A control system is disclosed for a mobile excavation machine operating at a worksite. The control system may have a locating device configured to generate a first signal indicative of a position of the mobile excavation machine, and a position sensor configured to generate a second signal indicative of a position of a work tool. The control system may also have an offboard planner configured to receive a first input indicative of a characteristic of an intended work area, a second input indicative of a characteristic of the mobile excavation machine, and a third input indicative of a desired change in the intended work area. The offboard planner may also be configured to generate an excavation plan based on the first, second, and third inputs. The control system may further have a controller configured to autonomously control the mobile excavation machine based on the first and second signals and based on the excavation plan.