There are some absurdly obvious ways to improve the T. One study was done in NYC which showed that making the busses free would actually save them money, as the gas/time spent idling (and delayed) actually cost them more than fares. I wouldn't go this far, but I'd say that if there are 50 people in line to get on a bus, that they shouldn't charge a fare to just get things on-time. As-is, I see bus drivers hold up things all the time for one person counting their nickles to get on the bus; that is simply inefficient. - http://www.economist.com/blogs/gulliver/2013/06/fares
Other places like Park St could be massively improved. Have one side of the platform (outer side), be the side that people get on the trains from, and the center area be the place that people get off the train. This would streamline foot traffic in the station. Make some stairways one-way to additionally streamline foot traffic.
For some reason, Boston never planned for bypass capability, for trains to be able to get around stations, run express or in parallel. NYC did it, and it helps a great deal with construction, disabled trains, express trains, etc... Not all the the T is 100+ years old, and for newer lines/stations such certainly could have been done.
I could probably sit here all day and think of basic improvements to help with things like this, but it takes the T forever to implement anything. How many years did it take to get the signs on the Red/Green lines operational for tracking train positions (a trivial problem in my mind, from an electrical and implementation side. These days, I'd just use iBeacons...)
And, you might have missed at the bottom of the page... here's a realtime version: https://mbta.meteor.com/