Thanks for responding. I'm afraid I haven't made myself clear; let me see if I can do better.
The issue is not the spacing of our metro areas in relation to one another (interregional distances). Rather, we have bad geometry withinour metros (intra-regional distances.) To me, this seems to stem largely from the many ways we've subsidized automotive transit and low density, single family residences since WWII.
The difficulty created by our development pattern is that you can almost never gather enough people into one place to justify building a train station, subway station, or even a bus stop. When you can gather them, it's normally by those people driving to the stop, and the disappointing crowd that shows up often doesn't pull enough weight to get reliable, frequent service to those stops. And as long as those people are going to get in the car anyway, and then have to wait a long time to catch the next bus/train, a lot of them are just going to say "the hell with it" and drive to their destination instead.
Alternatively, maybe you live in a downtown area where there actually are enough people in close proximity to justify transit stops with a high level of service. If you're in a typical American city, you'll run into the problem at the other end of your journey. Sure, you easily walked to your stop, but maybe when you get off at your other stop, several miles from the center of town, you're still several miles from the store, or the restaurant, or your friend's house. And it's typically not on streets that are pleasant to walk, because they're not very interesting and the cars may be quite fast. So you'll have to make your friend pick you up, or pay for Ubers both ways, or walk anyway in an act of defiance against the place you've ended up. None of that sounds great, and if you even did it once, you're probably thinking seriously about driving your car next time.
And so it turns out that what you really need are at least two places, neither of which really require cars, for transit to be all that helpful. And in the US, we seldom have that, because we have a single center of intensity, with the density decreasing radially in all directions.
These places don't have to be huge, either. A compact outlying town of 30,000 or so could reasonably have hourly bus service to the major city an hour away. The key is that the town needs to be walkable enough that people can easily get to the bus, and the big city also needs to be navigable without a car.
As to intercity: I'm not saying NYC and LA should have a dedicated rail line between them, but it would certainly be reasonable to have SF, LA, and SD all connected by rail, perhaps high-speed. But at the same time, given the spread out development of those three cities, it doesn't surprise me at all that that's not feasible.