Preface: If you live in SoCal and are flying to many places in Mexico TIJ is far, far cheaper than SAN, SNA, etc. It is very hard to justify paying the prices asked by the US airlines with this option available. Many Americans fly out of TIJ - it is a no brainer for many trips especially those with multiple passengers.

Volaris uses the Spirit/Allegiant model - you will pay extra fees, how much depends on how much research and planning you do. As stated earlier, AM is more like a US legacy carrier.

Volaris has non-stops on this route - AM involves a stop in MEX I believe. There's a lot to be said about taking a non-stop instead of a connection with backtracking. If you choose AM you can probably get business class on the TIJ-MEX route using Optiontown for about $30, this includes lounge access, shorter check lines, meal, bigger seat etc. A good deal.

The covered parking deck in TIJ is very close, safe and moderately priced - about 1400 MXN for a week. Another option is to park at Delta Truck Parking in Otay and cab it over (google this for details). I don't think this is worth the hassle but it depends on how long you are gone and what time you come back, border waits can be a few hours at busy times and it is faster to walk across. I wouldn't recommend the Volaris shuttle service from SD, your mileage may vary.

If you are an American you will need to buy a tourist visa at TIJ, about 300 MXN.