This won't solve the T's core problems, but I think a motivated in-house team could do world of good and I'm looking forward to seeing what comes of this. There's a lot of low-hanging fruit that can be tackled largely with software and cheap hardware. I informally interviewed for a summer job with the T and they mentioned a bunch of things that need work:
Green line dispatch is basically just some guy who sits in a chair and decides when to send another train out based on a loose timetable and gut feel. There's no single-source-of-truth about the state of the system, and information about delays and such only propagates as fast as human speech over radio. With better vehicle tracking in place and some cheap tablets, a lot could be done to manage this information more effectively.
Bus GPS updates happen on fixed 60-second intervals, on the same frequency as voice radio communications, so if the driver happens to be talking at X:00, the GPS update just doesn't get sent out for another minute. Lolwut.
Signal priority on the B and D is apparently going to be a thing in the near future which means integration with Boston traffic signals.
Developing faregate readers that support NFC and optical proof-of-payment methods as well as existing RFID cards. To be honest, this one seems a bit frivolous as the CharlieCard system works pretty well as is.
Beyond this, I can imagine a motivated team with the authority to knock heads together across departments being able to whip up pilots of Charlie RFID payment on commuter rail, pay-on-platform for a few busy surface GL stations, that kind of thing. If they can show people how nice these amenities are it could get the ball rolling on larger-scale ops improvements.
All of this stuff is chipping away the edges, but it's not all frills either, and could make a difference in real people's commutes. I ended up not taking the internship because as much as I love the T, I didn't want to take a software dev job in an environment that isn't really equipped to make and deploy software. If this announcement had come sooner I would probably have taken it.