The Phased Roll-Out: Yes, I know buses aren't the best thing in the world. I don't like riding the bus. Even so, this isn't a zero-to-100 thing. Someone's going to have to get on a bus - a whole lot of someones, actually. Stoughton extension to Taunton as a max-pain, highly accelerated build out. Get it built in 20 months, not 20 years. Extend every Stoughton train to Taunton, add four new inbounds and three new outbounds (one each way express). Don't screw around with electrification, DMUs or any sort of 'South Coast exclusive' equipment, but DO start running express buses from Fall River and New Bedford to downtown... via Taunton Station, so that people can transfer to a train. Let that service go for ten, five, or even three years - then push the three branches of South Coast with five new round trip trains dedicated just to them - the Fall River branch, the New Bedford branch, and the Hyannis branch.
I really like this idea. One of my biggest issues with the entire project is Taunton service depending on FR/NB service. That's one way to get Taunton service going while not completely ignoring FR/NB. You're also still able to get a feel for what demand there would be for FR/NB rail.