The San Diego terminal is terrible, other than it's pretty there. My first experience cruising out of there had a line going all the way down to the Midway. We were in the hot sun for a very long time. I think my PAT was noon, but I didn't get through the line til after 2:00pm.
My second experience was better, we essentially walked on. However, they didn't let us off the ship until quite a while after we docked. The traffic with taxis and shuttles gets really crazy, too. We parked at Aladdin lot and decided to walk to the dock instead of taking their shuttle. It's only a mile and quicker to walk.