Hey guys. Figured I'd weigh in here briefly since I grew up in Walnut Creek and also lived in San Francisco for a few years. Now I'm attending a law school out of state.
I won't weigh in on the rent prices too much, but you can definitely get decent one bedrooms in Walnut Creek near bart. I suppose the bart ride to civic center from walnut creek is about 45 minutes or so. If you don't mind that commute everyday, Walnut Creek is a nice place to live. The weather is great during the fall/spring/summer, and there are a ton of nice restaurants and shops and so on downtown. It's just a nice place to live. It may also be nice to live there to get away from the SF coldness/fog in the summer. YOu could also get affordable 2 br like you were looking at. Obviously check out the apartments before you commit to anything. Some of my friends apartments in walnut creek seemed nice at first, but then you realize they're more like a motel style place and you have people walking by your door all the time and you can hear everything above and below you. Also, some of the upstairs apartments can get super hot in the summer if they just have one of those on the wall A/C units. I'm sure youll find something good though; plenty of options there.
However, that commute can get tiresome, and it's also nice to actually live in the City so you can more readily enjoy all it has to offer. I lived in the inner sunset, and thought that the neighborhood was pretty decent. I lived one block from Golden Gate park, Cal Academy of Sciences and the DeYoung museum, 1 block from several muni lines that take you straight into downtown in about 20 min, and 1 block from Irving street where there are many restaurants, bars, etc. It's not the most trendy, but it's fairly safe and it's not that hard to get anywhere you need to go. Parking isn't terrible (full disclosure--i had a compact car), although if you're in the inner sunset you'll just need a parking permit, just like many other neighborhoods. Rent is fairly affordable there, and I imagine you could get a 1 BR for cheaper than the tower and it would probably be nicer. 2 BR would probably be a better deal if you can find it. There are a lot of choices of places to live in the city of course, but rent becomes an issue obviously. The marina, russian hill, lower pac heights, inner richmond, haight, panhandle, mission are all options for you, among others. Parking will be more annoying in the haight, panhandle and mission though, if you have a car. Marina isn't great either but w/e.
I second what others said about Richmond/Berkeley/Oakland/San Leandro/Hayward/Union City/Fremont. Avoid all of those except for certain parts of Berkeley and perhaps Oakland. Lake Merrit in Oakland is a nice, fun area and it's close to bart and quick to get into the city. depends on your taste though. Berkeley isn't bad, just have to find the right area. I've spent some time there but never lived there so i can't advise you on that.
You can also check out Orinda and Lafayette in the east bay. they are very nice suburbs, near walnut creek, and will be closer to the city. it's about 30 minute train ride from orinda bart to downtown SF, so about 35 min to civic center/hastings. There's not quite as much in orinda/lafayette as walnut creek, but they are nice places to live if you're looking for seomthing that is a little bit closer than walnut creek.