Boom assist management feature

A hydraulic control system is disclosed for an excavation machine including a tool linkage system. The hydraulic control system may have a first actuator configured to move a first link of the tool linkage system in response to input from an operator of the excavation machine, and a pressure sensor configured to generate a signal indicative of a pressure of the first actuator. The hydraulic control system may also have a second actuator configured to move a second link of the tool linkage system in response to input from the operator. In addition, the hydraulic control system may have a controller in communication with the pressure sensor, the first actuator, and the second actuator. The controller may be configured to automatically affect operation of the first actuator based on the pressure signal at times when movement of the second actuator is being requested by the operator and movement of the first actuator is being requested by the operator at a level less than a threshold.