I will second the review of Point Loma Seafood. There WILL be a crowd and parking is limited but it's worth it. The food is as fresh as you can get. I swear it tastes like they grilled it minutes after catching and cleaning it.
Another place I'd recommend if you're looking for an upscale dinner is The Prado at Balboa Park. I've had nearly every entree, appetizer and dessert ever served at the restaurant and have NEVER been disappointed and I tend to be a picky eater.
Enjoy your time here!

My wife and I actually went to Beach Break Cafe on your review and I don't know if anyone still checks this post but we wanted to thank you. This is definitely the best place I've had a sit-down breakfast outside of my wife's kitchen.
The service was friendly, quick and wonderful. The food was fresh, cooked just how we like it and while everyone recommends the coffee cake (which we loved) I think the Hash browns are the best I've ever had anywhere. Now people aren't going to go to a breakfast place for the hash browns but the portugese sausage, eggs, potatoes, etc are just amazing.
So thank you very much. We've just found our new home.