This isn’t a great excuse. The Berlin metro area is smaller than that, and had to contend with _being split in half_ for 40 years, and still has an infinitely better public transport system than SF, say.
By my comment I mean that the things GP list aren't the only things that separate SF public transit and Tokyo public transit. You'd also need crazy high population and density too.
I don't disagree with GP's list of things, I just think they're not exhaustive. They might be sufficient to get SF to Berlin level of public transit.
That said, to "beat BART" isn't a milestone for any public transport system anywhere. Except ... in the US, where even BART stands out as great. Hmm. Relatively.
(one part of me is kinda curious how the 101 would look like if you didn't do any work on it for 20 years. Mostly because it'd probably be a rather cool setting for some dystopian movie. Anyway ... transport infrastructure, whether public transport or roads, costs a f*ckton of money)