Supposedly the Connecticut DOT is pitching the idea of operating trains into Rhode Island (at least as far as North Kingstown) so eventually it may be relatively easy to go from boston to New York City without Amtrak...
Personally, I think Amtrak should operate a cheap service. Reserved seating only (to ensure that no unhappy customers find themselves in a cruddy seat), five-wide, and minimal amenities would very possibly be popular, and compete in a different market than the Acela and Regional as-is. At least one can get up and walk around a railcar, unlike a Megabus or one of the fabled Chinatown buses. Likewise, they ought to offer this sort of service around the country, where there are useful city pairs no more than 10 hours apart. Then again, I'm also a poor collegiate type with more time than money.
However, I see no reason why a commuter agency should compete with Amtrak over its own turf. Given that Amtrak, a quasi-governmental agency, is already attempting to compete with private (airline and bus) companies, and also considering that those private companies have fairly low fares, they ought to be the ONLY ones competing with them.