I've actually been tossing around something similar to that, Van, possibly inspired in part by your earlier proposals involving a D-E conversion.
First, build a connection between Riverway and Brookline Village. Ideally, put in a wye at Brookline Village, but so long as traffic from Newton can make it to Huntington, we're good. An extension of the Huntington subway also fulfills this requirement, but it's not mandatory.
Now, we have several options.
First: route all (or most) E line trains down the Highland Branch, and then down to Needham. This allows for an expansion of service, without disrupting capacities in the Central Subway and, theoretically, without requiring acquisition of additional rolling stock. Depending on project ridership of the Needham Branch, some fraction of trains could be "short-turned," diverted down to Heath.
Second: using the Kenmore Loop, divert C line trains around the bend, down to Brookline Village, so they run Cleveland Circle–Coolidge Corner–Kenmore–Brookline Village. The C Line has the lowest ridership of all the branches, and it is well positioned to take advantage of the Kenmore Loop. Anchored at both ends by connections to the D/E Line, and with a hub connection at Kenmore to the B Line, commuters will still have plenty of options to get to downtown. Furthermore, this will increase capacity in the Central Subway, either permitting increased frequency on any of the other three lines, or the addition of new service into the Central Subway. Likewise, with a shortened route, the Brookline Shuttle could probably be operated with a reduced rolling stock, freeing up cars for use on other, heavier-use lines.
(Optionally, the Kenmore hub could be enhanced by a Blue Line extension, especially if such an extension included express services. This would be great, to be sure, but it is not required.)
Third: the fun part: adding new [south-side] services. With the C Line diverted out of the picture, we have several options. A semi-resurrected A Line , branching off the B at Packard's Corner, just going to Oak Square, is one option. A more intense option would be a branch to Dudley, and/or a branch to the Seaport, following the loop-de-loop alignment which has been discussed previously in this thread. A dark horse candidate would be a semi-resurrected Arborway branch, possibly to Hyde Square, possibly to Jackson Square, or possibly all the way down to Forest Hills.
If we decide to go with any expansion that resurrects the Tremont Street Subway, one of the other three branches would probably terminate at Park Street, to avoid creating a bottleneck between Park and Government Center.
What about north-side service? Well, one downside of this plan is that it leaves the Boylston Street Subway a little underserviced. We can boost frequencies on the B Line some, but not that much. Even if we resurrect an A Line, that's still a one-third cut in service.
One way to ameliorate this would be to treat certain north-side routes as separate branches, and "short-turn" these services at various points.
These could potentially include Kenmore (though it's a bit difficult to short-turn there from the east), Packard's Corner (assuming no A Line, with the goal of increasing service to BU), or, my personal favorite, Brookline Village (in which case, the Brookline Shuttle would probably be curtailed to Kenmore, and just become a Beacon Shuttle).
(If a proper wye is installed at Brookline Village, service could even be run in a large loop.)
So, a potential service arrangement might look like this:
B: Boston College – Government Center via Kenmore
C: Brookline Village – Medford Hillside/Route 16 via Kenmore
D: Riverside – Lechmere via Huntington
E: Needham Junction – Park via Huntington
F: Dudley – Union Square via Washington
S: Cleveland Circle – Kenmore via Beacon
or this:
A: Oak Square – Union Square via Kenmore
B: Boston College – Lechmere via Kenmore
C: Cleveland Circle – Brookline Village via Kenmore
D: Riverside – Medford Hillside via Huntington
E: Needham Junction – Park via Huntington
