Ah, one of my favorite playgrounds. October is perfect timing, fewer visitors & awesome weather.
Balboa Park, where San Diego Zoo is located, is huge & has several museums & gardens in addition to the zoo. The Hillcrest neighborhood nearby has some terrific restaurants & independent stores. Not for the homophobic.
I love Coronado island. Nice, upscale village with restaurants & people watching & good strolling. I always enjoy a visit to the well preserved Hotel Del Coronado (rent "Some Like it Hot" before your trip). Several beachside walking/riding/blading paths with rentals. You can drive to it over the bridge or just take a ferry from downtown.
La Jolla. Del Mar. Carlsbad. All trendy beach cities, up the coast from San Diego & accessible by public transportion.
If you want something a little grittier, Ocean Beach & Pacific Beach are quite close (or maybe just neighborhoods in San Diego city) around Mission Bay, which offers dry & wet recreational pursuits. A non-weekend visit to Sea World on Mission Bay might be an option.
If you enjoy outdoor art, visit University of California, San Diego's campus in La Jolla. You'll need to get a map, the artwork is spread all over the very large, hilly campus. It's a great way to combine cultural & physical activity.
Nearby is Torrey Pines State Park which offers a variety of ocean bluff trails.
The Gas Light District in downtown San Diego has plenty of dining options. Close to downtown is the Mission District which is an historical area which seems bigger on tourism than history, but the strolling is good.
You have to visit Rubio's, there are many, for a fish taco or two.
San Diego has a mass transit system that should shame its neighbors to the north. In the core of the city there are trolleys. The Coaster trains run up the coast to the trendy beach cities. The main station is downtown, near the harbor, convention center & the Amtrak station. It's a very visitor friendly city but if you rent a car, plan for traffic.
Bring warm weather clothes though coastal fog might be a little chilly. Have fun!
Debra