It is not Amtrak that is replacing the standard station, it is the city and state government that is restoring an old station or building a new intermodal station which Amtrak then moves to. There are a number of new or restored station projects underway that have been funded by HSIPR, TIGER, development grants and state & local money. To list some off to the top of my head:
Denver Union Station (center of the Denver FasTraks transit system which has multiple lines under construction).
St. Paul Union Depot (Amtrak has not moved in yet, light rail line slated to start in June)
Raleigh, NC
Springfield, MA
Keystone East corridor: Middletown, Downington PA in the near term.
Newark DE
Birmingham, AL
Alton, IL
As for Miami, the Hialeah Yard will still be used to service the Silver trains and perform maintenance on Viewliner equipment.
Amtrak is said to move into Tacoma's Freighthouse Square commuter station after the Point Defiance bypass is built.
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