San Diego has some great Japanese restaurants. Most are in strip malls - if you want good food in San Diego, you likely will be eating in a strip mall. Try:
Kaito in Encinitas for traditional sushi - fresh and great variety of nigiri and sashimi, not a place for Philadelphia rolls, etc. It is about half an hour from downtown SD, but worth the trip. There is a long wait on Fridays and Saturdays, with reservations being largely useless:
130-A N. El Camino Real
Encinitas, CA 92024
(760) 634-2746
http://www.sushikaito.comIzakaya Sakura in Kearny Mesa. An unmarked Japanese restaurant with a huge and varied menu of small plates:
3904 Convoy St
San Diego, CA 92184
Wa Dining Okan in Kearny Mesa for homestyle Japanese cooking:
3860 Convoy St
San Diego, CA 92111
(858) 279-0941
http://www.okanus.comRobata-ya Oton in Kearny Mesa (same owner as Okan). Very traditional atmosphere - you will feel like you are in Japan:
5447 Kearny Villa Rd # D
San Diego, CA
(858) 277-3989