EDIT: Although, to be fair, the Valley and San Jose are way too low density to support a decent transit infrastructure. San Francisco's MUNI disaster is a problem of a different order.
There is a significantly different topography in the bay that greatly complexifies rail projects. Effective rail coverage on a large grid is not possible due to water and hill issues.
If low density is why San Jose can't support a decent transit infrastructure, then how can Denver do it with even less density?
I share your enthusiasm for the upcoming expansions, in particular the line to the Airport. The train is one of the big perks of living in Denver. It's awesome and only getting better.
Silicon Valley office space seems to be a little more spread out. When I was visiting a client in Santa Clara last year, I had to walk almost two miles to get to a light rail station to go have a nice dinner in downtown Mountain View. (And there were no buses available to cover that distance -- at least not that Google Transit knew about.)
(Disclaimer: My experience with San Jose is mostly limited to the airport area, and the Silicon Valley suburbs to the north.)
The CalTrain, which is the closest SF Bay equivalent to MTA commuter trains, stops in San Francisco, but far from local mass transit connections (either MUNI light rail or BART), to the point where there is an industry for private shuttles. This is a significant barrier to the adoption of commuter rail for people who work in the city but want to live further out.
Similarly, once in the Peninsula or South Bay, the CalTrain is often not near a mass transportation connection. Some of the major tech firms are located "near" CalTrain stops, but nearness is often at automobile-scale, as opposed to walking or cycling scale.
You need a pretty-damn-good local transit solution to support commuter networks.
Perhaps their citizens can not emerge from their bubbles far enough to believe it, but it's true.
The bay has regular bus service, sidewalks and bike lanes. Also trains. If you drive, you can do so from one place to another and find a parking place.
As someone who doesn't like to deal with cars, when I lived there it was very nice compared to the rest of the country, at least the 30 or so cities and towns I have lived in and the few hundred that I have stayed in for more than a few days, most of which it was extremely troublesome to get about without a car, and unlike San Francisco.
FWIW, I've lived in 9 cities in 3 countries across 2 continents. This includes San Francisco, and I can tell you, I've lived in metro areas substantially smaller than the SFBay and had better transit. There are many places in the US substantially worse, but there are also many others with a similar density profile or population size that are substantially better.