Part of the reason why we picked South Beach was to cut down the commute to South Bay (where I used to work when we moved to SF). Compared to South Beach/Mission Bay, Noe/Mission/Dolores is easily 20 mins more - mostly because you need to drive thru local streets. For North Beach, I would add 10~15mins more on top of that. It might seem like nothing, but 2hrs vs 2:30 hrs is a huge difference (and it does take that long very frequently).
Potrero/Dogpatch/Bernal is also good for both SF / South Bay commute. But for South Bay commute in general, nothing beats living near caltrain or other tech shuttle stops.