The only semi-unpleasant "your car is not available" experience I've had was with Alamo, and they didn't have our family's minivan (reserved on a dirt-cheap leisure rate). We eventually persuaded them to give us two midsize cars instead for no additional charge, however, which worked out fine.

I also keep getting automatics from Hertz in TLV when I reserve sticks. I think they don't trust Americans with sticks.