The secret is to use the Blue Line to get to the airport, not the Silver Line. So long as you're either on the Orange Line or don't have too many bags it's much faster.
Depends on where you live. If you live on the red line (I do) taking the blue line is almost always slower than the silver lie (sic). Remember that there's no red-blue connector, in fact the govt claimed that the silver lie was the red-blue connector because it went to the airport!
They have made noise about running the blue line to the Charles m.g.h. station, which would solve a number of problems. It would require a stretch of elevated line on Cambridge street right in front of Mass General, so no idea if it will ever happen.
A while back I saw a discussion about them running the current head space past Bowdoin down under Charles/MGH but the problem there was that the required head space would take it under the Charles and that'd end up being pretty costly due to the conditions there.