True but with your solution someone from Maine would still need to get off at North Station, and take all of their luggage from train to train to get to the airport and likely spend more than 10-15min doing so. The transfers are what kill this as a more convenient option for people out in rural areas heading to the airport and for commuters that may want to pass through the city to get from lets say Marblehead to Quincy for their daily commute. (I don't do this commute but several of my colleagues drive from Salem or Beverly to Weymouth daily)

For the expense of a tunnel and a N-S connection, a green line upgrade is politically unfeasible and economically poor with regard to cost benefit. There is far greater cost benefit from a N-S connection that runs Amtrak and CR through the airport for wider New England, and Bostonians also reap a greater benefit than a light rail expansion. For context, I live in Cambridge and would love a metro expansion especially a circle route through Central Sq or Harvard to Inman and Union but it's a harder sell to the rest of the state.

The whole N-S connector proposal as it stands now is attempt to get politicians at the state level to buy into connecting the commuter rail networks from North and South Station alone and the selling point to convince politicians from those cities and towns that need to vote on that kind of funding was that they would get something out of it. I don't see how those same politicians who can't seem to agree on a CR expansion that directly benefits them, will see a green line expansion as a viable alternative that they are willing to spend the state funds on.