A control system is disclosed for use with a plurality of mobile machines operating at a worksite having a resource. The control system may have a worksite controller configured to divide a common travel path into a plurality of segments, including at least a spot segment at the resource and a stage segment. The worksite control may further be configured to receive a first input indicative of a desire for a first of the plurality of mobile machines to leave the spot segment, and to direct the first of the plurality of mobile machines out of the spot segment based on the first input. The worksite controller may be further configured to receive first location information for the first of the plurality of mobile machines, and to direct the second of the plurality of mobile machines from the stage segment into the spot segment based on the first location information.