Or you could take the train... Amtrak operates a regular connection between LA and San Diego, You would have to find a way to get from airport to railway station in each city. (I looked at it, but was able to hitch a ride with a friend.)
BTW, about fares, shouldn't there be a link to an explanation in the main sticky?
My (SLF only) take on fare computation is:
- Route (from, to, one-way/return/multi-hop)
- Restrictions (advance booking, minimum stay, stopovers, special (student) fares)
- Availability (does the airline offer seats in that fare class)
If you are routed via a different hub there is almost no influence on tne fare, quite often direct flights are made more expensive.