I enjoyed Hotel La Jolla several times although it's been 2 or 3 years since I stayed there (858-459-0261... hope that number is still accurate). The rate was below $200. Rates may have increased though. Every room has a nice view of the ocean (the higher the floor the better for views). The hotel itself is a quarter mile or so from the beach. Just a few minutes west of I-5.
I've had mixed results on priceline when staying in downtown SD. If you're not familiar with priceline, basically you choose an area of the city, bid a price and, if they find a room at that rate they select the hotel for you. For downtown area I've gotten the Westin (good one!), Sheraton near airport (good) and the Radisson (fair). All were less than $120. Again, hotel rates have gone up lately and maybe those deals aren't available anymore. Balboa Park is a very short drive north of downtown.
I've never stayed at a hotel in Old Town. There are quite a few hotels in Mission Valley along I-8. One of the roads with lots of hotels on it is actually called Hotel Circle.
You might also try the Sorrento Mesa area. Lots of high tech offices there. Courtyard by Marriott and others that cater to biz traveler may have weekend deals. A little north of tourist attractions but only a ten or fifteen minute drive to get to Old Town and other attractions.