If MGH paid out money to help design the station, and they knew they wanted to have the Blue Line connection come in here, they should have paid more attention to the final design of the station.
I don't see it being easy to add a basement level (at the very least, it will require new elevators) at this point:
http://www.mbta.com/projects_underway/i ... _level.jpg
Anyway, I don't know that MGH is really a big reason for the Red-Blue connection project. They will be exactly half a mile away from the new Government Center station entrance, which is the typical walking threshold for rapid transit stops. Given that they are already right next to a stop (albeit on a different line), I think its hard for them to argue that they are underserved by public transportation.
No, the real reason for the Red-Blue connection at this point is to be able to more efficiently bring Blue Line Riders to points elsewhere on the Red Line and vice-versa. Many employment centers are along the Red Line, and such a connection would make living in East Boston and the other areas served by the Blue Line much more paletable for many -- especially those that work near the northern portion of the Red Line (i.e. Cambridge). Following this logic, the Silver Line really should connect to the Airport Station to bring Blue Liners more easily to the anticipated employment and recreation centers at the waterfront.
All that said, as I've mentioned before, the chance for the simple cut-and-cover BL extension is now long gone, what with the Cambridge St. reconstruction and the Charles/MGH station construction underway.
I don't anticipate this happening unless there is some later, major extension of the Blue Line. Where? Well if you get to Charles/MGH, you're pretty much pointed over the Charles River. Somehow swing back over to Lechemere and you could switch back to catenary and take the route of the planned Green Line extension. Yeah, I know, it'll never happen. I don't hold too much hope for a Red-Blue connection, either.