A worksite management system for use with a mobile machine is disclosed. The worksite management system may have a control module located onboard the mobile machine and configured to control operations of the mobile machine, and a controller in communication with the control module. The controller may be configured to anticipate a non-failure machine performance irregularity, and determine an adjustment to an operation of the mobile machine that positively affects the machine performance irregularity. The controller may also be configured to cause implementation of the adjustment before the machine performance irregularity occurs.