Any post-MGH extension of the Blue Line will all but certainly have to hit at least Kendall via a tunnel under the charles, just because selling a direct connection between Kendall and the Airport, East Boston, and whatever gets built at Suffolk is the single most useful thing that a Blue Line Extension can accomplish.
From there, it makes sense to hook left and tunnel under the Grand Junction ROW, which MassDOT already owns, and would be painless to tunnel under. If you want to add bus connectivity, drop in a station at the Mass Ave/Vassar Street interchange to serve the MIT dorms, Novartis, Astrazenaca, and all of the new commercial development happening north of Vassar and west of Mass Ave. From there, continue the BLX under the GJ, and split it roughly at the MIT Simmons Hall dormitory, with one spur breaking left under the MIT athletic fields, and the other spur continuing on via the GJ to West Station.
The "south branch" of the BLX can then tunnel under the MIT athletic fields and back under the Charles to Kenmore Square, where it continues under Brookline Ave with a stop at the old Sears building, before stopping right in the middle of the Longwood Medical area, with a station built under Brookline Ave between Longwood Ave and Francis Street. Now, in addition to connecting MIT and Kendall to the airport and Suffolk Downs, you've just connected Harvard Medical School/BI/BWH with MGH via a 1-seat subway trip, unifying the two halves of Partners Healthcare and the Harvard Medical-Industrial Complex, while putting them both within a transfer at Kendall of the main Harvard campus as well as MIT. In addition, you've just unloaded the Green Line Central Subway with a 5-stop rapid transit ride between Kenmore and Government Center that will take half the time as the same trip via Hynes/Copley/Arlington/Boylston/Park on the Green Line.