I've only been on the Thruway bus between Emeryville and San Francisco.
On the inbound trip, I scheduled my stop at Fisherman's Wharf. It took FOR-EV-ER, as traffic was heavy and it was the last stop.
So, for the outbound trip, I called Amtrak and changed my pickup to the Transbay Terminal. It was early in the morning, so the Uber ride didn't take very long.
I was a little nervous, as I get carsick on buses, but it wasn't bad at all. The bus was spacious, with HUGE windows, and it had better shocks than city buses. I could even see out the front window since the bus wasn't crowded. I thought the seats were pretty comfortable, and the bus driver was friendly. Plus, you get a great view of Treasure Island, Alcatraz, and the San Francisco skyline as you travel across the bay.