I still think the commuter rail of the future will be battery-powered. With today's technology, I suspect a battery-powered MU trainset could be built to handle of the MBTA's routes.
Getting OT, but hydrogen fuel cell would work great in this application. Typically FCV's have a generator powring electric motors, so you'd have the stop/start ability, but could run clean* fuel for long hauls. I suppose there could be a risk carrying compressed hyrdogen fuel into tunnels, etc though.
*depending on generation/distribution, etc