Bill - San Marcos, CA
First, it should be noted I don't use the shuttle. Since you are right across the street from John Wayne, it makes no sense to wait for it either coming or going. So, keeping that in mind I can't think of a better arrangement at John Wayne than the Hilton lot. Yes, you give up the roofed parking and yes, you have to walk, but you often have to walk anyway, and the onsite parking is usually so full you spend 10-15 minutes just looking or a space.
Booking at CAP you can pay half the price ( or less ) than you would at the airport structures, walk right across the street and cut directly through the middle of the parking structure, there is pedestrian access at the crosswalk leading into the airport and be at Terminal B in minutes, then walk to Terminal A or C as needed. When you get back no need to wait for the shuttle. You could, but it may take some time. I just walk through the parking lot, cross the street and am back at me car in just a little more time than it would take to walk to an onsite space. It really is the most convenient and affordable option I've found.