Just a quick point on making the existing green line heavy rail: right at this moment you could run a blue line train through the entire network, and aside from the platforms being too low (and possibly a few light fixtures) they would have no problems clearance-wise.
The only thing they can't do is the park street loop, which with heavy rail would be unnecessary. The east boston tunnel was built to the same clearances as the tremont subway, hence why the BL cars are such weird little things.
Kenmore and I believe Hynes were both built with high level platforms, with the pit then filled in. That's why the B goes slightly up then back down again pulling into Kenmore: that middle track is already high-level.
The C would have looped at Kenmore, the B between Packard's Corner and Chestnut Hill Ave abandoned, and the A extended out to Riverside as heavy rail via the B&A.
This plan could still happen today, in three reasonable(ish) steps:
1) Build a proper flying junction between Copley and Arlington where the old incline was for the E to merge in.
2) Extend the Huntington Ave subway to Brookline Village to tie in with the D out to Riverside
3) Extend the Comm Ave subway... somewhere. Either through Union Square to Brighton Landing then the B&A, or under Beacon Park through Lower Allston to Harvard , using the remaining bit of the Brattle Square tunnel, and completing Harvard's dream for a cross-campus subway.
All this could be done with service continuing as is. The only closure that would be required would be to raise the platforms / lower the trackbed in existing stations. 4 car blue line style trains would have no problem running and platforming at all stations, except possibly Boylston.
You would then have 2 heavy rail lines:
(A) Allston/Harvard - West Medford
(B) Riverside - Somerville
The D from Kenmore to Brookline Village could probably be tied in to the E down South Huntington, allowing trolley service to continue to Longwood and Heath Street (or possible reactivation to the Arborway).
The B could also be truncated at Packards corner in a Kenmore-style loop, especially if the Harvard subway was the chosen path.
You would then have a total of 4 possible trolley lines:
(B) Boston College - Packard's Corner
(C) Cleveland Circle - Kenmore Square
(D) Arborway - Kenmore Square
(F) Dudley Square - Park Street
^That one would use the Park Street loop and the outside tracks between Boylston and Park. The only issue with this plan is that the trolleys would have to cross at grade in front of heavy rail trains to turn around.
The Riverbank subway was proposed before the Boylston subway was built. The commissioners reports from the Boston Transit Commission back in the late 1890s crunched the pros and cons and decided it was a stupid idea to build way back then, just as it is now. Half of its potential service area is the river, it doesn't hit any major attractions, and it goes through a residential area without much room for growth. Exact same conditions over 100 years later. All the reports are on google books; its a fascinating read.
Converting the core green line to heavy rail is the only improvement that is needed, not the construction of an entire new subway. It would exponentially increase capacity and speed.