I agree that they'll need to take another bite at the EIS/EIR apple, but it's hard to see SCR Phase I creating the political impetus to do so. This is a project that depended in large part on geographic equity to push it ahead of other projects with much sounder fundamentals. Phase I will represent a $2 billion gesture toward geographic equity regardless of whether it works as transit. Once the inherent issues with Phase I start to manifest themselves in lackluster ridership stats, and the geographic equity card has already been played, why throw another billion towards what will look like a $2 billion sinkhole, when other parts of the state have much more viable projects awaiting funding?
Perhaps it will take a non-SCR proposal to create enough political cover to reopen the file in a timely manner. Maybe MA & RI jointly throw their hat in the ring, next time Amtrak's Corridor ID program is accepting applications, and put forward the idea of establishing a Boston to Newport corridor via the Phase II (Stoughton) alignment. The point of the Corridor ID program is create a pipeline of intercity passenger rail projects for future funding/implementation. There's no reason commuter rail couldn't use that alignment once it was built...it just can't be the reason to build it. In practice, though, it could create a nearer-term opportunity to reexamine the Phase II alignment and hopefully remove the insanity that the Army Corps imposed on it.
The proposed service would therefore need to be a new Amtrak route or else the feds would probably view the application as a trojan horse for a commuter rail project. Say it's a cross between the Downeaster and the CapeFLYER, and it makes six stops: Newport, Fall River, Taunton, Route 128, Back Bay, and South Station. At 70-ish route miles, it wouldn't be the shortest corridor Amtrak's approved through the program -- Charlotte to Kings Mountain, NC is half the distance, for example. And with similar pricing to Downeaster monthly passes (which are something like $80 cheaper than a monthly T pass for a rail trip of equivalent distance), it's not impossible to imagine reasonable year-round appeal beyond peak (summer) season, when Newport is in its glory.