The mindset of a cruiser is a lot different than that of a waterskier/wakeboarder. If you aren't riding behind the boat then you are likely to be on your way some place and the trip is a nusiance. To a cruiser, the trip is often the reason for having the boat!
The bigger the boat, the more important it is to keep track of the depth. From Stockton to Antioch it is pretty easy to stay in deep enough water, basically staying somewhere in the middle of the two banks. Once you get close to the Antioch bridge and all the way through Suisan Bay you had better be paying VERY close attention to the charts else you will run aground.
I wouldn't recommend going to SF and back in one day, and I would not recommend doing it if the winds were over 15 MPH. There are lots of sheltered areas to anchor for the night, and plenty of marinas where you can get a guest berth for a night or two. The fall is my favorite time for boating on the bay.