The MBTA already runs top speed on most of its lines once you get outside of roughly I95 depending on the line. Getting there faster would help but I don't think it would shave as much time off the end to end trip as you think. And for the urban stops they already accelerate and brake at the limit of what is reasonable for standing passengers. They can't push it too much or an old lady is gonna bounce off a wall and get a nose bleed and that's a bad look. It's not like Acela where a ticket guarantees a seat.
There will definitely be some improvement from electrification but I don't think it will affect median travel times much and the affect on average will mostly be from reliability.
The Fitchburg line did do upgrades a few years ago. I think they double-tracked sections that weren't. It still take a while--hour+--from the outer reaches.
Not enough seats is mostly pretty close into the city in my experience. At least on the line that I sometimes take, it's mostly Waltham in which doesn't have a mass transit line.
There will definitely be some improvement from electrification but I don't think it will affect median travel times much and the affect on average will mostly be from reliability.