I'm also curious about the commute time estimation.
I've been playing with the app around the Geneva area where I live and work and I think the commute times are a bit too optimistic.
Yeah, we are not accounting for connection times right now. However, we have the data to make it more accurate, just needs a bit more coding ;)
We take the times from cff / sbb site. We then add a walking time from and to bus / train stations. You can have a look to the graph here if you are interested : http://wonsch.ch/lab/2/