See
this (from Ari Ofsevit) for the Red/Blue connector that I'm envisioning.
I agree 100% that the plan for a deep bore tunnel is a waste. But a cut-and-cover train tunnel that ties into Bowdoin is largely comparable to a cut-and-cover pedestrian tunnel that ties into Bowdoin, as far as cost goes.
The State is proposing the sketch in red. You and I agree that's ridiculous. You're proposing a version of the blue sketch for pedestrians. I'm proposing a version of the blue sketch for trains. The only difference between blue sketch for trains and blue sketch for pedestrians would be
slightly larger tunnels. All of the access and egress and etc. (where so much of the overall cost lies; see: the Green Line Extension) is the same for trains as it is for pedestrians.
And pedestrian tunnels aren't even that much more narrow than train tunnels. The pedestrian tunnel at Terminal A at Logan is actually
wider than a Blue Line tunnel would be, for example. One walkway plus one moving walkway is roughly the width of a Blue Line car. The "station" at Charles /MGH would require a wider tunnel to accommodate a center platform, but that width wouldn't be necessary for most of the length of the tunnel.
Also, neither plan includes a turnaround for trains.