The Inbound vs. Outbound convention gets confusing the closer you are to the core, but out in Somerville it seems like the clearest way to explain the direction.
I've brought this up before, but it seems like there would be benefits of not keeping the B-E convention fixed from terminus to terminus. Why not do something like have B-E as the termini in the SW, then have 1-4 as the termini on the other end (e.g., 1=Medford/Tufts, 2=Union, 3=Government Center, 4=Park Street)? Then each train gets labeled with a letter and number showing its two termini, allowing trains from any terminus on one end to serve any terminus on the other. That way you could mix and match, for example, "D1" trains, "D4" trains, "E1" trains, "B3" trains, etc.
This would allow more operational flexibility (e.g., if there's a track issue at Fenway it won't shut down service at Ball Square) and also allow more flexibility for riders (e.g., someone who lives in Allston but works at Cambridge Crossing will only have to change GL trains about half of the time instead of all of the time).