Maybe one suggestion I could think of, would be a risk score. Given a set of segments, which transfers are the most "risky"? (From those departures, arrivals and transfer estimates, how bad would the impact be going forward from missing a transfer?)
The main thing I get from Google Map's estimates is an indication that something has changed. If google gives me a route I wouldn't expect, it's normally because some trains/busses have been removed from the schedule today/running slow. Without forcing a route on you, it would be nice to have it hint at the fact that I'll be catching the last train that hour, thus making segments before it "riskier", scaled by how often they arrive + how long my transfer time is + how out of sync they are from the next segment's departures.