1. Direct - They have the least stops and are the fastest. They don't go into towns. They go around them. 2. Express - They only stop at the largest towns. 3. Regular - They are the slowest and stop at every town.
You then use timing to make sure that they don't crash. The slow train will generally stop on the track and wait while the direct overtakes it (you don't want them both moving at the same time).
This isn't new. It's be around for 100 of years.
If you have three cities on a perfectly straight line, you can run your high-speed trains as above.
If the city in the middle is not on a straight line path between the two end cities, now your train tracks need to curve to connect the three. If you make the curve a large enough, smooth enough curve, it won't hurt your maximum speed much, but when you're talking "1000 km/hr" ... and in any case, you're also adding miles to your route, and if you make your route 20% longer to weave from city to city along the way, you are also make it 20% slower.
Non-stop is an important element of a truly fast train. Firstly because you don't want to be constantly stopping and starting, but also because you don't want to detour your route through a dozen cities which aren't conveniently on a straight-line route to your destination.
So if you want to make a train run as fast as possible between Boston, NYC and DC, you're telling Connecticut, New Jersey, Pennsylvania, Maryland, and maybe Delaware, "Hey, we want to take a big chunk of your land for our project, and no, we don't want our super-fast trains to stop at any of your cities, and we can't even run a slower train because making the tracks actually go through the right parts of your cities would slow down our fast trains too much."
Have fun with your negotiations!