Do you like having a garage? If so, you will likely get further away from SF. With a shuttle, living in Fremont/Union City is nice as you can get 3 bed/2bath+garage for 1800, where you can pay twice that or more for a 2/1+1 parking _spot_ in SF. You can move further out and get more space for less, but the commute, even on a bus gets long.
I grew up in Fairfield (50 miles east of SF), have lived in Sunnyvale, Fremont, Redwood city and Milpitas and have typically been happier further from SF than closer, that said, Sunnyvale was nice. If you want Warm + walking distance to night life you should also check out downtown San Jose depending on where your shuttle picks up.