Flying into San Diego, we used Alamo and were very happy with them.
Flying into LAX, we used National and had no problems. They seemed to have the fewest numbers of shuttles. We had to wait quite a while for the National shuttle. We had seen some of the other rental company's shuttles 2 - 3 times before we saw a National shuttle.
Flying into ONT, we used Budget. (Memorial Day weekend) National was bad enough, but Alamo had a long line. But Budget really did not have their act together and it took quite awhile.
The ONT trip -- we used Budget because we booked through hotwire.com. We got a really good rate on an SUV. It was just slightly more than Alamo wanted for a regular car.