I grant you the custom gauge issue. That's unforgivable. Labor costs (Janitor earning quarter mill) are something they can work on --They just seem unwilling to go the union-busting way. Passing tracks, I'm not aware of most Caltrain stations having passing tracks --they just schedule things so far apart they can pass at a couple of stations. I'd prefer more frequent service.
A ring around the bay or a second Transbay tube would alleviate the Transbay bottleneck.
On the plus side it's all electric and works with minute headway.
BART is a costly system and they've been masking the true costs for decades by deferring maintenance, the $3.5B they've gotten from taxpayers is just a portion of what they need to bring the system up to date. And worse, they can spend up to a third of that on operational costs... which are sky high in part because BART is saddled with high labor costs and can't rein in its union's lucrative work rules. Case in point, the Warm Springs station is not even open yet, but it's fully staffed, including janitors to clean an empty, unused station.
But the problems don't end there -- BART's equipment is non-standard gauge so every order is a custom order with high lead times and there's no world market for BART's gauge. While Caltrain is able to supplement capacity by buying surplus cars.
And BART is designed with no passing tracks, so there's no such thing as an "express" train. Want to go from San Jose to SF? Well you've got to stop at every station in between. While with Caltrain you can take a 5 stop "baby bullet".
And finally, the capacity of nearly the entire system is dependent on how fast passengers can get on and off the trains at Embarcadero station. BART has a billion dollar band-aid for that, by digging out the other side of the station so passengers can board from both sides. What they really need are multiple tracks, like what Caltrain has at their SF station (and other high volume transit systems throughout the world)