I ride the Metra Milwaukee District West line daily. While the station density is slightly less, we have a much higher average speed. MAS is 70 mph and the engineers try to get there every chance. If the distance between stations doesn't permit getting there, it's accelerate until you need to start braking, No dogging it between stations because the distance is short.
The post above mentioned the long stretch west of West Roxbury. We crawled through there at 15mph tops. No trains to meet, no extended stations stops due to loads, just plain slow running. This was the 9:15 train which had one car open with about a dozen people on the upper deck. An equivalent train on my Metra line, running slightly more frequently (hourly), would probably have 3 or 4 cars open, all loaded at least 50% (some parties sharing seats but not too many).
Anyway, it sounds like for whatever reason, MBTA has the speed limit on the branch so low, it can't help being a slow trip.
Larry
Reno, NV (yes, I've moved)
ex-N&W Sandusky, Ohio