"Upgrade the system to support more trains" is easier said than done.
For one thing, BART is running ancient rolling stock that's already well pasts its original designed service lifetime - the bulk of the fleet is now sixteen years over its original 25-year service life. The system breaks down frequently because of this, and over the years the system has lost enough cars (and cannibalized enough for parts) that there is no longer sufficient spare capacity to rotate into service when trains break down.
Couple that with track and control design that does not permit bypasses, and you've got yourself a recipe for trouble. A train stuck in the tube cannot be bypassed - unlike other subway systems - and thus every single minor trouble cascades into a major cockup of everyone's day.
So you have a system that is prone to magnifying small failures into big ones, and you combine that with trains that are way past their service life and running on proverbial fumes.
Bonus also: BART hasn't purchased any new rolling stock in a very, very long time, and all of its rolling stock will come up to the end of their service lifetimes by 2019 (with 65% of the fleet already past service life). Instead of spreading the capital cost of new vehicles over decades, BART is now placed in a position where it needs to replace its 670+ car fleet in the span of about six years. In all likelihood this will mean even more of the fleet going into "beyond service life" territory and wreaking havoc on everyone's commute.
BART can be improved. But before BART can be improved you first need to catch up on 20 years of complete neglect. It's billions of dollars that has no hope of ever getting spent in the current political and economic climate, and that's just to get BART to the point where it's reasonably good at accomplishing its current stated purpose. At that point you can think about expanding the system, increasing capacity beyond its current scope, etc etc.
Actually, I just looked this up, the current plan is to phase in new vehicles beginning 2017, over a 15-20 year period. That's going to be quite a treat, considering even the newest trains in the current fleet will be 44 years old by the time BART is done with their rolling stock refresh - 18 years past its expected service life.
Bonus also: large parts of BART track are actually substantially damaged, reducing speed and increasing noise (to unsafe levels, even). You can't hope to begin adding capacity until you fix this. Between the fleet, the antiquated control systems, and damaged track, BART doesn't need minor fixes, it needs deep overhauls of nearly every aspect of its infrastructure.
MUNI isn't much better off: http://www.sfexaminer.com/sanfrancisco/report-on-munis-light...
Ancient equipment, ancient infrastructure, a fleet stretched thin to the breaking point, decades of under-funding and mismanagement, all of these descriptors apply just as much to MUNI (if not more) than to BART.
The regional and city transportation infrastructure in the SF Bay Area is a complete mess. This is, unfortunately, not hyperbole. We are over a decade, and billions of dollars of additional spending, away from even restoring these transit systems to proper function, much less go after expanding their scope.