Some ideas:
Wouldn't worry about staying around the San Diego State Univ area, because there are lots of good freeways to zip around on.
Family Fun Center:
I think it's around intersection of the 15 freeway & the 52 highway.
It's miniature golf, battle tank tag (shoot & disable the other guys' moving tanks as you you drive in your own tank, w/ tennis ball canons)
Balboa Park: You could easily spend 2 full days there & not see it all. A really pleasant place to be. A local like her may enjoy showing you around it. Lots of good museums, hands-on science center, IMAX theater, zoo (you said that's out), Olde Globe Theater, Air Museum, good Mexican restaurant, etc.
Go out to Scripps Aquarium in La Jolla. Worth seeing. From there drive over to Glider Point & watch guys hang gliding with their dogs, and in tandem with girlfriends, etc., then go walk around & dine in La Jolla village, which can be romantic, and interesting things happening there.
The whale center & lighthouse at the end of Point Loma is sort of boring, I'd skip it, but if you're scraping for an inexpensive good sight it sort of works.
Visit the old Hotel del Coronado, huge old wooden hotel on the beach, Coronado Island, hang on the beach in front of it, eat there. She might like that.
Gaslight District is a tourist thing with lots of bars.
There's a reconstructed "old town" . . .I forget it's proper name. Lots of old 1800s buildings have been moved to one place near base of a hill, you pay admission, walk around, everybody dressed 1800s style. I'd skip it in preference for Balboa Park attractions.
Avoid Tiajuana. Maybe Ensanada if you must see Baja, but better not. Maybe drive down as far as Raul's above the beach, south of TJ, then escape back home before the Federales make you pay them or throw you in jail.
Go up to Del Mar, see the horses, if you want to $$$ go straight inland from Del Mar, around Mary's Tack & Feed & hot air balloon in evenings.
Generally, around San Diego, more north is better, toward Del Mar, Encinitas, Rancho Santa Fe. Or inland Ramona / Julian, but I think that pine forest area recently burned up.
