Top speed (mostly) comes from the tracks, not the method of motive power.
As it stands they're already maxing out and exceeding (when they're late) the max speed for the class of rail they have.
Some of the inner stops might get a few seconds faster with better acceleration but that's about it.
The grade crossings are also kinda f'd. At full speed you can be in the middle of the train and see the arms still be in the process of lowering at certain crossings. That ain't safe. Faster won't make that better.
Top speed, sure, but for typical commuter heavy-rail, a non-express train isn't running at top speed for all that long.
Diesel-electric trains take a LOT longer to accelerate compared to a modern EMU, so much so that Caltrain's electrification project shaved 23 minutes off the SF to San Jose local trip, from 100 to 77 minutes.
Videos [0] [1] make the acceleration improvement pretty clear.
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.
As it stands they're already maxing out and exceeding (when they're late) the max speed for the class of rail they have.
Some of the inner stops might get a few seconds faster with better acceleration but that's about it.
The grade crossings are also kinda f'd. At full speed you can be in the middle of the train and see the arms still be in the process of lowering at certain crossings. That ain't safe. Faster won't make that better.