I find the same limitation to be a pain for California flights.

SJC/SFO/OAK with an option for SMF would be nice for Norcal.
LAX/ONT/BUR/LGB would be nice for Socal.

It gets especially hairy for NYC-CA flights. I use beta.itasoftware.com and it works great.

qsf;smf::b6 is the search term for the Norcal airports; ::b6 limits the results to b6

nyc;swf;hpn works for EWR/JFK/LGA/SWF/HPN for any carrier

qla is the code for LAX/SNA/BUR
qla;lgb;ont would add LGB and ONT to the search

The time restrictions on beta.itasoftware.com are also great for those trips when I need to be somewhere at a certain time.

I have no vested interest in the site, I'm just a satisified user of it.