At Boylston a decent number get off but I don’t see a lot of people backtracking to Hynes. I’d imagine the Parcel 12 construction’s relocation of the stop has made that transfer less convenient for folks and they’d rather go to Kenmore or Copley for service downtown or out to the branches (This is in contrast to the wall of people that go from Hynes to the 1 northbound that I’ll get to later).
This might seem like nitpicking in an otherwise excellent analysis, but I really doubt that people were walking all the way from Mass Ave to Kenmore or Copley for Green Line transfers. Yes, going from the southbound 1 stop to GL Hynes requires 2 pedestrian crossings and walking over the Pike, but that's still much more efficient than walking
12 minutes to Kenmore or
12 minutes to Copley. Perhaps it may be that these crowds blend into the (vast) pedestrian traffic rather quickly, and are thus less noticeable?
Another possibility is that for many people (especially from Cambridge), their
destination is in the Back Bay area, so they're not using a Green Line transfer anyway. They could be working or shopping there, and my guess is there's high demand for both, given how there
always seems to be a good number of passengers waiting at northbound Hynes at all times. Whereas people taking the 1 between Hynes and points
south (most likely BMC) probably aren't going to Back Bay and are instead transferring to GL, and therefore the NB alighting passengers you see immediately enter the station.
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Also circling back to the point
@TheRatmeister made earlier about the Albany St (Cambridge) and MIT stops being "underwhelming" compared to Central and Harvard, my guess is that the Albany St stop is heavily commute-focused. Most of its ridership comes from the nearby pharmaceutical companies, like Novartis, Pfizer and possibly all the way up to Area Four. A smaller group comes from apartments to the west along Albany St, most of which house MIT students (so they might be less reliant on transit and contribute less ridership). Your methodology only uses ridership for the entire week - I'm not saying that's a bad metric in itself, but I'd guess that checking only weekday (or weekday rush hours) ridership may give higher numbers.
But yeah, the triangular area bounded by Mass Ave, Albany St and Main St hosts a lot of jobs and is underserved by transit. The Red Line passes by without stopping.
The MIT stops are obviously used by MIT students and staff. I think there's decent student traffic between MIT and Harvard on weekdays, but as
@Koopzilla24 said, some of them may have taken the M-2 or biked. On weekends, you'll also see some undergraduate students taking the 1 south to Back Bay for shopping, and possibly north to Harvard Square. On another note, MIT students are more likely to stay in Cambridge (even near Lechmere or along the eastern parts of GLX corridors) than across the river in Back Bay or Allston, at least according to the subleasing ads I've seen.
Anyway, it shouldn't be a surprise that they don't compare to Central's ridership, because the latter has a rapid transit connection. You can have people from Alewife and Davis taking RL and transferring to the 1 for Back Bay, for example.