Tunneling to Brigham would probably be a Phase I under any burial plan, so for purposes of getting anything done in the future that is probably a first step you have to eventually do and digest before going further. Tunnel itself is cheap under the reservation; it's of course the stations that are going to drive up the price (I'm going to take a reliable guess that Northeastern is going to push for 'palatial' instead of a couple more quaint little Symphony setups). And yes, Brigham does need to become a surface Blandford-like stop if you're portaling-up.
What you may want to do is cut 1 subway stop out of that. Entrance-to-entrance spacing Kenmore-Hynes, Hynes-Copley, Copley-Arlington, Arlington-Boylston, and Copley-Prudential averages about 1900-2000 ft. shortest walking distance (Kenmore-Hynes the high outlier, Copley-Arlington the low outlier if the Berkeley St. entrance is open). Pru-Symphony and Symphony-Northeastern are only 1350 ft. entrance-to-entrance or subway entrance-to-surface crosswalk, and the other E reservation stops keep to 1200-1300 ft. between nearest station crosswalks. Subway headhouses on both sides of the street save the need for a crosswalk and light cycles at a crosswalk, so the spacing needs are a little bit apples/oranges surface vs. subway. And the platform placement underground does not have to correspond with any particular block...the headhouses do.
So with that in mind. . .
Northeastern
-- Place the platform under the Forsyth St.-Forsyth Way block.
-- 4 headhouses, 2 across-the-street pairs flanking both ends of the platform, Arlington-style (albeit without such a long Berkeley-equivalent walkway). This will be a crush-load station every hour between classes so the separate fare lobbies helps swallow the short-duration crowds.
-- 1 pair of non-invasive Arlington-style easterly stair+elevator headhouses on the corner of the
Speare Diamond grass and that
little patch of grass across the street, literally staring mid-block at the current surface platform.
-- 1 pair of westerly headhouses on the corner of the
MFA's front lawn, and diagonal across the street at
Hallenborg Way.
Congratulations, you just consolidated 1 stop without making anyone at either stop walk longer distance when crosswalk time gets factored in.
Longwood
-- Underground platform more or less where the current platform is.
-- 1 fare lobby at one end with 1 pair of across-street headhouses.
-- Headhouse in front of
Mass College of Art, likely grafted on/into the building. Across-street headhouse in front of this park at the
Ward St./St. Alphonsus corner.
Absolute zero change in walking distance for Longwood station patrons.
Brigham (surface)
-- As-is, except the staggered inbound platform gets moved up across from the outbound platform and the Wigglesworth St./Hospital crosswalk has to get moved to the Worthington block (better spacing anyway) because the portal mouth goes at Wigglesworth.
When it is time to do Phase II to Brookline Village, your subway stops would be. . .
Brigham
-- Platform more or less underneath the circle.
-- 1 lobby.
-- Across-street headhouses
opposite ends of the circle. Any opposite ends will do.
Mission Park/Riverway
-- Platform wherever it best fits between the 2 current stops on the Parker Hill Ave.-Riverway block. Location subject to change depending on tunnel alignment into Brookline Village.
-- Probably only 1 side-of-street headhouse, given difficulty of doing across-street pairs around the row houses.
-- 2000 ft. entrance-to-entrance spacing is the
gas station at Riverway. Pros: Can loop buses and/or South Huntington trolleys on the surface right in front of the headhouse in an efficient transfer setup, more ridership, immediate Emerald Necklace path connectivity (good bike cage station candidate). Cons: only about 1200 ft. walking distance to Brookline Village station.
-- 1600 ft. entrance-to-entrance spacing is the
courtyard in front of Mission Park (knock out that last chunk of brick wall by the driveway and it's all grass in a 100'x100'x100' triangle. Pros: more even station spacing between Brigham and BV. Cons: less transit connectivity, very low ridership for a subway stop, Mission Park residents may have a legit beef about a headhouse with a view into their rear bedroom windows.
-- NOTE: Depending on tunnel alignment to BV you may for engineering reasons be locked into one station entrance location to exclusion of the other, so cover your butt by gaming out either option.
I think if I had to choose and the engineering left me with a choice I'd take the gas station with surface transfer because it's got multiple transit lines, a busy corner, path connectivity, more breathing room, and less abutter concerns. Even if it is a little close to BV. If BV's going to be the line-split superstation and Urban Ring anchor, I don't think it's that big a deal to have Back Bay-Prudential like spacing between the major station and the very minor station. But engineering/EIS for the tunnel will probably answer that station siting debate conclusively one way or the other, so probably not worth worrying about today.