Agreed. If you use DB or NS (Germany and Holland) website, they seamlessly include long distance, high speed, bus, and regional trains, and often S-bahn (commuter). See the example below:
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The itinerary was made on purpose between smaller destinations in two countries, and I chose the most complex one just to illustrate a point. As you can see, it arranges an itinerary from commuter train to HST to regional carrier to private access carrier to commuter train. In each case it will also tell me what car I'm in, what track the train arrives on, and what track the connecting train departs on. This makes it much easier to travel by train.
What's really crazy is that the software is for NS, the Dutch railways, the trip originates in Germany, and it finished is Austria, and involves four carriers providing transport and a fifth providing booking. That's a lot of moving parts and it works.
I'd love to see Amtrak work commuter train schedules into their reservation system, perhaps even sell connecting tickets with a $1 convenience fee (of course marked "connection not guaranteed" or something). Once I met a lady on the CofNO riding New Orleans-Hazel Crest to meet her family. She thouhhy that she had to ride all the way downtown and walk across the loop to Metra Electric. What she didn't know is that she was riding back out an hour in the reverse direction on the same rails. I showed her how to transfer at Homewood and saved her a few hours.
Given that all passenger carriers get some federal money, it would be wise for them to require integration to some extent on ticketing applications, at least in the corridors.
The new Acela: It's not Aveliable.