With Waze, it almost always tells me to get off the highway at a certain point and then take a parallel (smaller) road to work. If I, as I now almost always do, ignore it and drive past the exit to take one couple miles down (and much closer to work) I can see Waze's ETA dropping by a few minutes. I complained to Waze about it, bit don't see any changes so far.
OT: I'm livid at all the efforts to punish drivers for driving (like the toll etc). We aren't driving for fun! I bet most of us would prefer not driving. I try to work from home when possible because driving in commute hours is a terrible waste of time.
I don't have big problem with tolls, as long s they are not on taxpayer-funded roads, and actually get you something. Not just the privilege of crossing the bay instead of driving around the Bay.
I've had Google Maps (desktop web browser) give me a route once through heavy traffic, but when I dragged the route to a mostly-parallel highway, my estimated time decreased by 10 minutes. So it's not perfect, or they wanted more users to give more data on the traffic.