I'll probably always take the train into Boston. Even though it's a little more expensive than taking a greyhound or driving (if I can find parking), I don't like to drive in Boston.
However, if I needed to go much further I'd be in a bind. The website is really difficult to use at times. I was trying to get to Maryland(?) at one point to buy a used car, but I couldn't find a page that would show me stations near where I needed to go. I ended up finding one nearby using Google, and though the Amtrak website allowed it as a destination, it seemed there were never trains headed there. After 15 minutes of confusion, I checked wikipedia and it turned out the station had been closed to trains for years and only operated as a museum.
So even if they redid the rails, they might have to redo the website as well.