We rented a car from Fox rent a car from the san diego aiport. As others have also told you have to wait for around 30-60 mins before you get their shuttle.

This shuttle took us to a creepy looking office. Tha parkign space where the cars were parked was dimmly lit. We had asked for a Mustang and as usual they did not have it and they offered us free upgrade. The frustrating part was that he did not have enough vehicles to choose from for an upgrade. We finally decided (due to lack of options) to rent a Prius (which actually is cheaper than a Prius in terms of its cost, I don't know how it qualifies as an upgrade, lol). We did not take their insurance as we had our own GEICKO.
Due to the lighting conditions and our impatience (we waited there for more than an hour just trying to get that car) we just had a cursory look at the physical condition of the car. After driving some distance we actually noticed that the car bumper was chipped of the paint on one side. We rented the car for 5 days and then returned back; we did not have any accident/incident. The rental guy inspected the car and checked it in.
After 3 months we got a call from the collection agency that we owe them approx $5500 for damages to the car. On investigation they said that
1. the rear seat belts were missing (we never used the back seat and as such never noticed whether it was there or not)
2. The car door is scratched and so they replaced both the doors.
3. Loss of income due to inability to rent the car during repairs & admin fees

FYI you can get a brand new Prius for approx $20,000. So we were charged with more than 1/4 price of the car for a damages which we don't know ever existed while we had the possession of the car and for the damages which were never found during their checkin inspection.

(FYI most car rental agreements have it that they can inspect the car post delivery at their time of convenience, but before renting to a new customer).

Now comes the even crazier part of it. When we contacted our insurance guys, they talked to us in a tone that implied that this is very normal practice most car rentals follow to make money and most of the legal clauses in the agreement put you in a position from where they are always right and we are always wrong.

Lessons Learnt:
1. Don't rent a car unless there is no other option
2. Rent it from an agency which cares more for its reputation
3. Irrespective of your insurance status, buy their insurance, and you might be saved of all the deductible and possible premium increase situations
4. Inspect the car thoroughly, take its pictures, and best thing I would suggest to everyone is to make your own template of car rental agreement with your clauses written and ask their guys to sign it (If we can get it it would be great)