As another ex-san franciscan (and would be returner if the housing weren't so darned expensive), there are some really wonderful things about the city. I'll second the notion of looking for a hotel around Union Square - there are quite a few that will fit the bill in the under $200 a night range.
Another great photo location if you have the time is to go out to the very end of Geary Boulevard. Just before it bears to the left and goes downhill past Cliff House, you'll see a parking lot on your right. Pull in there and park. If they've finished restoring the stairs, you can walk down the hill there to the remains of the old Sutro Baths, where there are some really great photos, including Seal Rock, which is about 30 yards out in the surf (DON'T go in! that area is prone to some very nasty violent undertows that will suck you right out into the Pacific). Come back up the hill and walk out the path that exits from the opposite end of the parking lot where you entered. Follow that path along the clifftops - you'll get some wonderful views of the Golden Gate, and when you get farther along, the Golden Gate Bridge. About 2/3 of a mile or so along, there is a nicely rebuilt staircase that will take you down to the beach at the bottom of the cliffs there. You can get some wonderful shots of the bridge from the beach. The stairs are steep, and not for the faint of heart or the out-of-shape. If you go early in the morning, mostl likely it will be cool and foggy and misty. If you hang around 'til midday, the fog will burn off and you'll have bright blue sunny skies. If you get a rental car, you can drive over the Golden Gate Bridge and take the first exit. Follow the signs for the Marin Headlands. The road (Conzelman Road) winds along the clifftops on the Marin side of the Golden Gate. You can get some spectacular views back over the city from there. There are a number of World War II batteries built into the tops of the cliffs that you can get out and explore, including tunnels through the clifftop. I don't think she's around anymore, but when I lived there there was this woman who would go up there on weekends and do this aboriginal throat-singing in the tunnels, to the accompaniment of a guy playing a digeridoo. The main tunnel there had a nine-second reverb, so you'd get these amazing echo effects. Google "The Tunnel Singer" and see if she still performs there.
For great ethnic food, head out to the Mission district - up and down Dolores and Valencia between 16th and 18th, and some of the surrounding streets, have fantastic Latino cuisine. If you like Cuban, get there EARLY (5:30 or so) and go to Cha Cha Cha in the Haight - it's at 1801 Haight street, right near the beginning of the panhandle of Golden Gate Park.
There's an animal menagerie (I hesitate to call it a full-blown zoo) in Golden Gate Park that would keep your daughter happy, and you can get some photos of American Bison while you're at it.
For meals, there are a ton of fantastic places to eat all over the Bay area... do some quick searching once you've settled on where your hotel will be, and check out
http://www.sfsurvey.com/rr.asp
to find some restaurants within walking distance of your hotel.
AVOID Fisherman's Wharf. Not only are the hotels overpriced, the traffic (on the streets AND the sidewalks) nightmarish, but most of the restaurants are total ripoffs as well.
For a very nice Italian dinner, go to Vivande Porta Via - 2125 Fillmore. It's more quiet, out-of-the-way, and outstanding fresh food.
If you want to do Alcatraz, go online and look up booking tours. If you book in advance, you can book a night tour (or late evening as the case may be). The great thing about the night tour is that A: you can only book it online, you can't buy it at the ticket office, so there are fewer hordes to deal with on the tour, and B: you can get in to see some areas of the prison that are normally off-limits during daytime operations. I did the night tour, and we got to see the prison Hospital, including Al Capone's sitz bath where he was treated for hemorrhoids, the operating table where "Doc" Barker died being treated for wounds sustained while attempting escape, and Robert Stroud's large suite of cells where he kept his research. The prison Pharmacy still has the old wooden cabinets typical of a 1930s drugstore, and it even still smells like a pharmacy.
http://www.parksconservancy.org/visit/alcatraznight.php
