I would suggest crew fatigue be essentially rolled into the maintenance mechanic, such that maintenance clock puts a modifier on crew grade and or task force training. A year of overhaul to reduce four years of active service (a length unheard of in my empire) is an nice shore leave, for instance. While I don't object to the concept, what could amount to an additional clock that regularly needs attention doesn't really add much. We already need to tool shipyards (1-6 months), build ships (a year, or more, sometimes), train them (1-2 years), and then overhaul (4-8 months out of the gate, just to fix issues after training). Ships must be overhauled for approximatly 25% of their active service time (not in port).
Thats already a lot of down time, and since all of my maintenence is done at citizen'd colonies, they don't need any more.