The place along the route that most needs the service is Union Square. I think it makes by far the most sense to extend the Green Line there along the Fitchburg, and leave open the possibility of a future extension to West Medford via a Prospect Hill tunnel or a branch.The Tufts kids can walk to Davis, and West Medford has the commuter rail. If the route is just built out the Lowell Line, that's too far from Union Square to effectively serve that population.
IMHO, one big problem not mentioned in the Union Square routing is
the area between the former B&M Yard 8/7 "Red Bridge" and Medford
Street. What's the problem? Well you have to figure out a way to get
over or under McGrath Highway and CSX's Grand Jct Branch at
Swift Interlocking.
Hmmm. If you want to be able to extend the line under Prospect Hill, the Green Line will have to be on the north side of the Fitchburg Line anyway. Take down the Red Bridge and put in a viaduct, using part of the bridge's approach embankment. Biggest problem I see is that the Fitchburg ROW may not be wide enough.