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Oh, yeah, that's a tough one, but seems workable.
It doesn't seem so technically difficult if you can get the transit data. The phone GPS supplies your current location for the bus version, or alternatively you can just identify the most recent stop you saw. San Francisco has around 1000 city buses (I looked that up a while back) and you can put fairly precise coordinates, bus number, and route number of a bus into 4 or 5 bytes. So the complete locations of all the buses is around 20K which is less data than the javascript bloat that nextbus.com sends on every new visit. You do want the route maps (from transit agency) and street maps (openstreetmap) but overall it's not huge.
Yeah, and things like arrival times could be flipped around, so time until your stop is also just the ETA of that bus to the stop anyway. Just changes to how you slice and dice the same data.
There might be other buses ahead of the one you are on, en route to that stop. You really want the phone GPS to figure out what bus you're on, maybe showing a selection of possible bus numbers or route numbers. It would be great if you then see a route map showing your location as you move.