What's your plan?
https://upload.wikimedia.org/wikipedia/en/6/67/California_to...
That said, you start having lots of connections and the value of transit systems goes down. I was just looking last night and I'm told that the time to get from SFO to the Santa Clara Convention Center/Great America/Stadium is still about 2 hours which, while theoretically doable, isn't something I'm going to do.
Millbrae is the largest 'intermodal' station west of the Mississippi (https://en.wikipedia.org/wiki/Millbrae_Intermodal_Terminal). It is the closest station to the largest airport in the Bay Area (SFO). If you're flying into SFO and want to connect to the high-speed rail, Millbrae is the _most_ accessible station, and one of the few (only?) stations in the region which allows you connect to most of the Bay Area.
'Poor parking near the bart station' - BART says there are 2900 spaces available. I don't know what would be expected, but I wouldn't describe that as 'poor parking'.
Also, perhaps less relevant, Millbrae is the last stop on the existing rail corridor still allowing relatively flat (and straight) tracks. North of that, tunneling or large bends around hills may be required.
It is not the closest station to sfo; that's San Bruno, or at least that's how the trains go the majority of the day.
I would suggest putting the high speed train station in the same station that BART & Caltrain share. If I lived in SF and wanted to go to LA, I would just hop onto a BART for 20m and then catch the high speed train. I would also expand the BART parking tower to several more floors if possible.
Bart is already oversubscribed for many times of the day and shitty. Further, it's more like 35 minutes (San Bruno to Montgomery is 27 minutes; I know that bec it's my commute.) Bart also is hostile to people with luggage for much of the day, and with high-speed long distance transport you need to assume people will be bringing more than a backpack. Hostility: lack of space on the train, lack of good elevators, lack of clear directions to navigate the stations. Bart also lacks clear signage or directions, particularly for people from out of town or who don't speak or read english. And finally, bart is just flaky and shit. There are weekly 10-20 minute system delays, monthly 30+ minute delays, and quarterly system shutdown for hours. All of which is annoying for commuters, but a deal-breaker when attempting to connect to long distance transport which presumably is relatively infrequent and hence requires you to be on time.
Europe mainly decided to route trains through city centers, sometimes by also taking the strategy of using older, low-speed track for the urban portion of the trip, and accelerating to high-speed once the train switches onto the new tracks. However even there sometimes the outskirts option was taken when geography makes it more convenient; examples include Gare de Saint-Pierre-des-Corps (outside Tours, France) and Köln Messe/Deutz station (outside Cologne, Germany).
It's already sorta-kinda connected to Union Station by MetroLink (regional commuter rail).
Millbrae is also obviously not the best location in the bay area to stop. Millbrae population: 22k. sf population: 837k.