If you look closely, there are two big branches of commuter rail in the Boston region--north and south--and they do not connect at any station. If you want to travel from one branch to the other, you have to get off commuter rail and onto a metro train, then get off the metro train and board a different commuter train in order to continue your journey. And the three-seat journey includes dumping you out into the busiest metro stations, the literal hub of the entire regional transport system, so it's a pain in the ass. Most people don't bother, and for good reason.
The two branches should clearly be connected to maximize the network, at least via a tunnel between North and South stations, and perhaps out between Brandeis and Auburndale stations as well (if that's possible).
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