While I agree with most of your digs (and the mayors Brown definitely had a lot to do with Bay Bridge decisions), the east span replacement was definitely needed for seismic reasons. The question was: plain highway bridge at a few billion$ (think San Mateo or Dumbarton style) or architectural/engineering masterpiece at around 10? And it turned out not to be such a masterpiece in several respects - will be maintenance-intensive.

As for rail capability: the original Bay Bridge rail was anything but rapid transit, was suitable, only barely, for the time, and is long since gone. There was no reason for the East Span to have any kind of rail capability. Adding it would probably have doubled the price, at least, and then what about the old west span? Nobody's going to revert the bridge to car traffic on the upper deck only to make room for streetcar-speed transit; dream on if you think otherwise. And the YBI tunnel has been modified for vehicle traffic on the upper deck that restricts clearances on the lower so rail can't be done there any more. What's needed is a second BART tube, possibly (in a dream world) with capability for main-line rail (HSR to use it at a normal rail speed) - if you want something railish and think you can find the money (would make everything spent on BART so far look like pocket change), try for that.