I second the recommendation for Zuni in San Francisco. Ive been going there for 20 years and have yet to be anything but delighted. I always try to hit them on mileage runs or even with brief stops at SFO. I will sometimes arrange an early flight and grab a cab or cheap rental car and go to Zuni for dinner and come back to SFO and get the redeye. And yes, the chicken is great but so is everything. They somehow manage to get better east coast oysters than places in Manhattan and I cant figure out how
Another very unusual place is Greens. It is right on the Bay with fantastic views of the Golden Gate Bridge (from parts of the restaurant at least). They specialize in vegatarian food. Note, Im not at all a vegatarian, but I find the food unique and interesting.
Having said that I should add that I havent been to Chez Panisse in about 3 years so this is a little dated. However, I have been there maybe 10 times in the last 20 years. I have also been to about half of the top restaurants in Paris, all in New York (save a new one we are planning to hit in August) and several in Tokyo and London. Unless things have changed very recently, go to Chez Panisse. It is one of the top restaurants in the world, and one of the most inventive. Im not sure what you saw bad about it but I would be very skeptical of it unless I was very confident of the source. It is just stellar in my experience.