So the penalty I'm calculating is the stop penalty of slowing from a cruising speed to a dead stop, waiting at the station, and then speeding back up to cruising speed versus maintaining cruising speed the entire distance; you can think of this as the time penalty that the Route 128 stop generates (being on a nice straight track that allows very high speed).

What you're talking about instead is the penalties imposed by a more constrained right-of-way in urban environments. Except when we're talking about Philadelphia (or most of the Northeast in general), you can't really escape from a constrained right-of-way anyways--a quick crayoning suggests you're adding about 20 miles of railway route which, even at 200mph, adds more time than you're saving by itself.

Consider again the cost of bypassing to save time. How many millions of dollars are you willing to save a minute of travel time? It is far cheaper to put that money into straightening the worst curves of legacy inner city track than to spend it bypassing the city altogether, not even accounting for the loss of revenue by not serving what are objectively large cities.

Is there anything existing that avoids having to stop the whole train at each stop? For drop-offs, just detach the back train car at a stop. Everyone who wants to get off just moves to the back train car at each stop. For pick-ups, some relatively high-ish speed coupling to add a car at the front of the train. In this way, the train loses one car and gains one car per stop. And as the train progresses, it also slowly turns around, ready for the return trip. Sidings at each stop can allow the boarding and un-boarding process to happen without tying up the track for through-traffic. Seems like something like this must have been tried at some point. Why is this not a thing?

It would remove all flexibility in capacity between different towns, and require most people to move to a different carriage at least once after boarding — which is especially inconvenient with bags. Even if you couple the carriages at high speed, how do you connect the doors between them sufficiently safely to allow people to move along the train?

The coupling of modern high-speed trains is also a significant part of their crash safety. Keeping the train connected if it derails means there's less chance of a loose vehicle punching through another. (See how e.g. [1] has most of the vehicles pretty much intact.)

I think in most cases, running an express train followed by a stopping train is good enough.

[1] https://assets.publishing.service.gov.uk/media/547c9037ed915...

Old HSR, yes. Maglev? No.

The issue is that steel wheels on steel tracks doesn't provide enough grip to accelerate, so the train takes a lot of the time to get up to speed.

Maglev, meanwhile, uses a linear motor, so you can accelerate very fast if you want to.

I think the bigger constraint would be noise. Wikipedia talks about a 70dba noise limit in residential areas after protests and such, but doesn't say what speed exactly they're running at to meet that.

70dba is rather a lot, though, I imagine you'd end up with a lower limit in the US since I don't think most people are going to be easily convinced that another inter-city transit method is going to be worth the noise to them.