A control system is disclosed for use with a machine. The control system may have a first linkage arrangement, a first actuator, a first interface device, and a first control element. The control system may also have a second linkage arrangement, a second actuator, a second interface device, and a second control element. The control system may further have an input device selectively activated to generate a mode signal, and a controller. The controller may be configured to selectively generate commands directed to the first control element based on only the first actuator signals, and to selectively generate commands directed to the second control element based on only the second actuator signals. The controller may also be configured to selectively generate commands directed to both of the first and second control elements based on only the first actuator signals an in response to the mode signal.