An engine system, comprising: a plurality of combustion cylinders in an engine; an exhaust gas aftertreatment sub-system fluidly connected downstream of the plurality of combustion cylinders; wherein deactivating a portion of the combustion cylinders (53, 54) changes the temperature and hydrocarbon content of an exhaust gas stream in the exhaust gas aftertreatment sub-system; an engine load module structured to detect an engine operating state of an engine and generate an engine status report; a timing module structured to receive the engine status report and generate a cylinder request after the engine has been in a certain engine operating state for a certain period of time, wherein the timing module is structured to determine that the engine is operating in a low load operating condition for a certain period of time based on the engine status report, and wherein the cylinder request generated by the timing module includes deactivation of a portion of combustion cylinders based on the low load operating condition existing for the certain period of time; and a cylinder module structured to receive the cylinder request and generate a cylinder command to be sent to the engine to deactivate the portion of combustion cylinders based on the engine operating state existing for the certain period of time, such that an exhaust gas temperature threshold corresponds with when cylinder deactivation mode is initiated after the certain engine operating condition has been detected for the certain period of time, wherein the cylinder module is structured to generate a cylinder command to reactivate the deactivated portion of combustion cylinders responsive to the engine status report indicating that the engine has been operating with a load greater than a preset threshold for a certain period of time, such that the engine is operated with no deactivated cylinders, and the cylinder module is structured to provide a thermal management command during the combustion cylinder deactivation mode to increase engine exhaust gas temperature, wherein the thermal management command is provided while the portion of combustion cylinders are deactivated such that the thermal management command complements the cylinder deactivation mode, and wherein the thermal management command includes at least one of retarding an injection timing, external hydrocarbon dosing, a post injection of fuel after the combustion event in the cylinder, a wastegate opening, a closing an intake throttle, a closing an exhaust throttle, and increasing a speed of the engine. a plurality of combustion cylinders in an engine; an exhaust gas aftertreatment sub-system fluidly connected downstream of the plurality of combustion cylinders; wherein deactivating a portion of the combustion cylinders (53, 54) changes the temperature and hydrocarbon content of an exhaust gas stream in the exhaust gas aftertreatment sub-system; an engine load module structured to detect an engine operating state of an engine and generate an engine status report; a timing module structured to receive the engine status report and generate a cylinder request after the engine has been in a certain engine operating state for a certain period of time, wherein the timing module is structured to determine that the engine is operating in a low load operating condition for a certain period of time based on the engine status report, and wherein the cylinder request generated by the timing module includes deactivation of a portion of combustion cylinders based on the low load operating condition existing for the certain period of time; and a cylinder module structured to receive the cylinder request and generate a cylinder command to be sent to the engine to deactivate the portion of combustion cylinders based on the engine operating state existing for the certain period of time, such that an exhaust gas temperature threshold corresponds with when cylinder deactivation mode is initiated after the certain engine operating condition has been detected for the certain period of time, wherein the cylinder module is structured to generate a cylinder command to reactivate the deactivated portion of combustion cylinders responsive to the engine status report indicating that the engine has been operating with a load greater than a preset threshold for a certain period of time, such that the engine is operated with no deactivated cylinders, and the cylinder module is structured to provide a thermal management command during the combustion cylinder deactivation mode to increase engine exhaust gas temperature, wherein the thermal management command is provided while the portion of combustion cylinders are deactivated such that the thermal management command complements the cylinder deactivation mode, and wherein the thermal management command includes at least one of retarding an injection timing, external hydrocarbon dosing, a post injection of fuel after the combustion event in the cylinder, a wastegate opening, a closing an intake throttle, a closing an exhaust throttle, and increasing a speed of the engine.