I can't believe that I only recently learned about the Copley Square of the 1960s - converted into a hideous concrete plaza of levels, and a mistake thankfully undone:
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I see a lot of parallels to City Hall Plaza. I'm sure the designers of this lovely centerpiece of urban life were well-educated architects too.
I love all of your suggestions for ways to break up Government Center into parcels. Given the complexity of building over the Brattle Loop, and considering that tight turnarounds like that and (ex-)Lechmere constrain the type of LRV able to be used, I think Brattle is an acceptable/inevitable jettison, made up for by adjusting service levels (necessary in light of the GLX anyway). I had sketched an idea out for realigning the Green Line tunnel previously in Paint, mainly to show that if you got rid of those and the fountain you suddenly have quite a lot of solid ground to work with:
But looking at
OpenRailwayMap, I wanted to go one step further. This is partially Crazy Transit, but I think fits well into a discussion of how to redevelop Gov't Center. Here are the Plaza tunnels as they currently exist, and then with demolition of the active GL tunnels:
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Tie the Green Line Northbound into the abandoned tunnel where it forks South of the Sears Crescent, and then build a new southbound tunnel parallel to the existing ones, running back up "Cornhill". This keeps the rail ROW on the pedestrian throughway and parallel to the OL, minimizing the footprint:
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As the GL and OL are on two different levels, you can construct a new station closer to Congress Street within the "bulb" of the new GL loop, with platforms oriented as outlined here (red lines indicate stairs/elevators from the upper GL level to the lower OL level):
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To tie into the existing BL platforms, you could construct a pedestrian walkway as part of the new Southbound GL tunnel that descends to the BL grade. Conceptually, I also really love the idea of opening up a sightline from the courthouse to Faneuil Hall via this corridor, which means opening up a part of Center Plaza as outlined. You could design the headhouse for this realigned station to have stunning sightlines of emerging from the ground to see one to the West and the other to the East:
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You can also design this station to fit well into the NLRB. If the Congress Street alignment is used, it's directly adjacent. And while this is almost a lateral replacement for Government Center, because you're tying in the Orange Line, there are also a number of ways to consider consolidation of nearby stations for service reasons. Instead of also using Milk/State station as it exists now, you could eliminate those OL platforms and re-route the existing entrances as walkways to the new City Hall area. I think this makes a little more sense than the current spacing between the DTX and State OL platforms.
(Vanshnookenraggen's map for context.)
E: Come to think of it, if you did that, perhaps it makes more sense to connect to the Blue Line platforms at State instead via this walkway. Then the Blue could skip the current GC platform and go right to Bowdoin (and then eventually proceed to Charles St. when Red/Blue is built).
E2:
Here is a diagram of the Adams Square platforms. The track to the far left (closest to the City Hall elevators) may be usable for most of that haul, with a new tunnel curving West at where it currently loops East. It doesn't look like The EGE sketched out Milk/State, but
here is a diagram of the station as it exists (although, this is missing
the entrance at 28 State St which would be to the far left of this diagram). It'd be a bit of a hike, but you could block off these existing State OL platforms, but retain the entrances for a covered pathway to the Blue platforms. Then, where the Oak Grove OL platform is now, extend the platform North as a walkway to the new Oak Grove "GovCtr2.0" platform and station. It does mean that this new station would kind of be Milk/State/Devonshire/Adams/Scollay/GovernmentCenter.