[ak217]

Caltrain is not "already pretty good". It has antiquated, overweight trains due to federal requirements and the fact that it shares track with freight traffic. Those trains can't accelerate properly, so those "convenient" stops in each downtown mean the trains can't run with enough frequency. There are not enough trains and too many at grade crossings, which produce severe noise pollution (due to the federal horn sounding requirements).

Caltrain is WAY overdue for upgrades. The electrification project, which will solve some but not all of these problems, is in need of a speedup. Many at grade crossings need to be replaced with bridges (and some are being replaced), but because of all the fiefdom-like towns along the way, getting anything done along the right-of-way is a nightmare.

Although there is no tractable way to merge Caltrain with BART (because of BART's own foolish planning decisions, such as a custom gauge), and you're right that there is no space for a second right-of-way, there is another neglected project that would benefit here: Dumbarton Rail (http://www.bayrailalliance.org/dumbarton_rail). At various points it was suggested that either BART or Caltrain should be extended across that bridge - either way, completing that link would add badly needed capacity in a region that has long neglected its traffic infrastructure.