Question:
Why is it so crippling? Whats the makeup of your empire?
Personally, my first wave of colonies are all mineral based, then I start specializing worlds. Planets with low accessibilities but nearly every mineral become maintenance bases-- even if that means maintenance ships and automines, with fuel stockpiles. Every one of my systems has at least one Ship House, with enough maintenance facilities to keep at least system defense boats up to spec.
As such, I never really have run ins with maintenance concerns except for after long training missions. It takes a MONTH to bring a ship out of overhaul early. Woah! As such, I don't like long downtime, so they all get overhauled as a fleet on a return from any sortie (fix the micrometeorite holes, crew shore leave, etc)