Did you actually take a look at those plans? A subway loop in the mud of the Wharf? Backtracking from the north and then you are missing the center of the Marina?

The plans look like they were drawn up by Rose Pak from the other side of the pale.

And then use your best imagination to picture how you would lay out a grade separated wye underground north of the presumed Washington Sq. station. The gradient is downhill toward Ghirardelli and then you need to know how deep is the tunnel at Washington Square. Would appear very challenging. The last thing you would want would be an at grade wye undergound. Dumb.

A line from Lombard & Fillmore connecting under Pacific Hts. to a line on Geary(with its vastly greater patronage potential)definitely should show up in their plans if just for comparative purposes. It would be more direct and faster with fewer station stops on route.