I use GLX 4-10x per week, because I live on it, so honestly I can't speak for others why it's not as "popular" (for the record, getting on at Ball Square, the second stop on the line, at 8AM means not finding a seat anymore), but I can take an uninformed guess.
These stations/neighborhoods are positioned in the system/region (like other branches of the green line and ends of other lines) where they would greatly benefit from strong cross-city/urban ring transit connections. The radial nature of the T, with all lines and branches leading downtown, really promotes only using the T to get into work or a night out downtown (...until ~1AM).
If someone from Allston is looking to get brunch in Union Square, the green line isn't an option when searching up directions from a random apartment in Allston, but bus trips up to 52 minutes long are suggested (26 minutes is the quickest transit route, which isn't bad at all, but relies upon having some luck or diligent planning to match up with the schedule due to frequencies). A car ride is 13 minutes. To get to Ball Square - most options are busses only (44 minutes being the shortest currently), but at least this time one option includes taking the green line for a total commute time of 76 minutes, vs. a 19 minute drive.
I suspect the bus network redesign will improve these options, but that relies upon to the T to a) hire hundreds of staff and b) increase promotion of taking the bus. I personally still have a hard time getting some friends to trust me that the bus is safe, reliable, and quick, when I've never really had a problem with them, apart from their frequencies and dropped trips. If the goal is to boost economic development in neighborhoods around Boston, the next set of expansion projects after Red-Blue and NSRL should focus on creating a less radial transit system.
Also, a nitpick here - if I were a small grocery store, as Ball Square Produce is, I wouldn't really expect an explosion of customers, until TOD around the station brings in more permanent residents. Not really sure how many people will take a trip out to Ball Square for some moderately-priced produce and nuts, when someone can likely find a similar shop closer to them...