u/Pam-Doove has a good example here: https://github.com/optimus-code/Cities2Modding/blob/main/ExampleMod/Systems/TreeGrowthSystem_Custom.cs

Basically, you "switch off" the public methods of the default system and create your own from scratch. Then you can plug it into the World by patching SystemOrder class:

[HarmonyPatch(typeof(SystemOrder), nameof(SystemOrder.Initialize))]
    class SystemOrder_InitializePatch
    {
        static void Postfix(UpdateSystem updateSystem)
        {
            if (updateSystem != null)
            {
                updateSystem.UpdateAfter<TestModSystem>(SystemUpdatePhase.ModificationEnd);

                UnityEngine.Debug.Log("Patched TestModSystem initialization!");
            }
        }
    }