Merge Caltrain into Bart?

  the large budget blow-outs that are 100% certain to follow

That's way more of a BART tradition than Caltrain. Just look at the SFO and Oakland airport extension debacles, let alone the clusterfuck that is Santa Clara county rail (both BART and VTA rail). VTA rail ridership is so bad, they've actually painted over window exteriors so that the lack of passengers can't be seen from outside.