I lived in San Diego for five years so I can give you some advice. If you're planning to do the major attractions: beach, sea world, san diego zoo. I recommend Mission Valley. Easy access to all of San Diego with tons of shops, grocery stores, and reasonably priced restaurants. Downtown and Gaslamp is more party central. As for the Bahia, I would avoid Pacific Beach/Ocean Beach with small children. It's just not that safe on the weekends or at night. Go to Mission Bay for a clean, family safe beach. Hope this helps.
