A machine control system for use with a machine having a power source and a transmission is disclosed. The machine control system may have a clutch configured to connect an output of the power source with an input of the transmission. The machine control system may also have a sensors configured to generate signals indicative of machine operations, and a controller in communication with the clutch and the sensors. The controller may be configured to determine the current machine application based on the signals, and vary an actuating force of the clutch based on the type of machine application.