I don't know about La Jolla hotels but downtown hotels often charge hefty parking fees ($20-$30+). On the plus side, you can get to many places by public transportation. We stayed at the Hyatt next to the Marriott by the convetion center,while my wife attended a conference. Later moved to the Omni (got it through Priceline; could not use Priceline during the conference due to the whole area being booked). La Jolla is pleasant (do see the Scrippts/UC San Diego aquarium) and you MAY avoid high parking fees,but will need to drive to get to many attractions,including restaurants and museums in SD itself.

BTW, the Omni was excellent, and right next door to Petco Park.