My understanding was SNA is limited in terms of departures/arrivals due to noise restrictions in area (neighbors), and is the primary DISNEYLAND airport, thus UAL can price it high and people will pay it (the flights are almost always packed between SFO-SNA).

ONT was added back to United's routes from SFO for the "Palm Springs" season, as they hope people will fly into ONT then make the awful one hour drive to the Desert (as opposed to flying direct on Alaska into Palm Springs).

Before there was the SFO-ONT direct route, you had to do SFO-LAX-then a prop plane to ONT (which they often cancelled if not enough reservations). Many an SFO colleague of mine got stuck at LAX with no way to get to meetings in ONT when the connection was cancelled, as driving there would take FOREVER.

Basically there is no rhyme or reason for Nor Cal-So Cal fares......I can fly out of SFO or OAK, and I always check BOTH airports, as sometimes one is cheaper than the other, depending on your So Cal destination (and who can explain the BUR fares???).

Frontier has recently begun flying out of SFO.....so it seems like that may be helping out on SFO-LAX fares of late.....

PS......SNA is the best of all the So Cal aiports in my humble opinion (except for the overwhelming smell of McDonalds that permeates the United gates)