I guess I didn't ask that right.
I take it that there will be several types of trains: Amtrak operated Amtrak LD trains, i.e. the Vermonter; Amtrak operated (on behalf of the State of Connecticut) Springfield-New Haven shuttles; and the new service CTRail/ConnDOT whomever operated (on behalf of the State of Connecticut) Hartford line service between Springfield and New Haven. Each of these three categories is a different operation, right(?), with different, but some overlapping station-stops, and different fare structures?
So if I were at some intermediate point in Connecticut, say Berlin or Hartford, and wanted to go to NY City, I could buy a ticket using any of these trains, but depending on whose train it was and whether I wanted to go to Penn Station or Grand Central, there would possibly (probably) need to be a separate ticket for the New Haven to New York portion and the fares are going to be different. If all three of these services have different pricing/ticketing policies, aren't trips like this going to have a confusing variety of prices, the more so if you are going to someplace common to Amtrak and Metro North, like Stamford instead of NY City.
If the Springfield Shuttles and the new Hartford line service have different fare structures, isn't the State of Connecticut essentially competing with themselves? Assuming that the various trains are evenly spaced, rather than competing head to head, this will mean that a trip to Stamford or NYC will cost arbitrarily different amounts depending on when you take it and could require different kinds of tickets.