Here's a map I made detailing expansions to the system mainly along or under existing RoW. This sort of build out is probably the least expensive way to widely expand service on the T without lots of tunneling beneath urban roads rife with underground utilities.
http://goo.gl/maps/uHgGb
The Red Line is expanded northward in a trench cut under the Minuteman Bikepath, which would be replaced by decking the train trench, like the SWcorridor linear park. There'd need to be a section of bore beneath Arlington center, and a tunnel or bridge for the 128 crossing. It could end in a big park and ride development linking to Hanscom and the Rte 3 corridor, or continue beyond a 128 transit center and continue to the Burlington Mall, which would entail running along a utility RoW and tunneling to the mall. Definite stop locations would be at Arlington Center, Arlington Heights, Maple St in East Lexington, Lexington Center, I-95 and Burlington Mall. Depending on funding and local support there could potentially be stops in East Arlington at Lake St and North Lexington at Bedford St. The Ashmont Branch would move to the Teal Line.
The Blue Line is brought to the Northeast through Lynn to Salem. My map has it routing to the Commuter Rail RoW after Wonderland, although it could go through Cedar Point as well. I envision stops at Riverworks, Lynn Center, East Lynn at Chatham St, Swampscott and South Salem at Jefferson Ave. Potentially the line could stretch further to Salem Center, though this would add considerably to the costs. To the West after Government Center, the line runs under Cambridge St to Charles/MGH to a trench cut in the footprint of Storrow Drive, which would be either eliminated or downgraded (the resultant traffic flow from such a move has been discussed extensively elsewhere). The Blue Line would follow the Storrow footprint to Mass Ave where it would bore under the Charlesgate and terminate at Kenmore Square. It would eliminate Bowdoin and stop at Charles/MGH, Esplanade by the Hatch Shell at Arlington St, Darthmouth Landing between Dartmouth and Exeter, Charlesgate between Mass Ave and Charlesgate, and Kenmore. There would be potential for expansion beyond Fenway to Allston/Watertown/Waltham or Brighton/Newton.
The Orange Line would take over the Haverhill Line to Reading. The Commuter line would route along the Lowell and Wildcat instead. The Orange Line would keep Haverhill's stops and add a park and ride at 128 by Quannapowitt. The most difficult aspect would be grade separation on the way to Reading. Out of Forest Hills the line takes over the Needham line through Roslindale and West Roxbury until Millenium Park where it terminates. It could potentially continue into Needham.
The Indigo Line would operate using DMUs or EMUs. Upon the construction of the North-South Rail Link, beneath the NEC, South Station and the CAT the Indigo would run through a portal to South Station's underground platforms and on to North Station exiting out of a portal behind BS&G and joining the Fitchburg Line where it would run short turns to Cedar Woods at 128. Another Indigo branch would run along the Framingham Line from Riverside.
The Teal Line is a new HRV line combining the Mattapan Line, Red Line Ashmont Branch, N-S Link, GLX and Lowell Line to Anderson. It would continue out of Mattapan in a short bore tunnel to the Fairmount line and run beneath it to Readville, where it would then run along the RoW into Dedham, terminating at the Bos-Prov Tpk. Some of the route along the Lowell Line requires large projects to get rid of grade crossing. It would stop at Anderson, Mishawum, Montvale Ave, Cross St, Winchester Center, Wedgemere, W. Medford, Mystic Valley, College Ave, Ball Sq, Lowell St, Gilman Sq, Brickbottom, Inner Belt, North Station, Hanover/Haymarket, Aquarium, Rowes Wharf, South Station, Broadway, Andrew, JFK/UMass, Savin Hill, Fields Corner, Shawmut, Ashmont, Cedar Park, Milton Village, Central Ave, Mattapan, River St, Fairmount, Readville, and a pair of stops in Dedham.
The Green Line would see the most changes.
- Restoration of the A Line to Oak Square.
- Potential to complete old route to Watertown.
- Restoration of E Line to Forest Hills.
- Completion of GLX to Union Sq Somerville. Extended farther to Porter Square.
- Potential for running to the Watertown Branch to Watertown Sq.
- Bury B Line to Packards.
- Bury E Line to Brigham under RoW.
- Bury E from Brigham to Riverway as a bore tunnel, continue bore to link to D at Brookline Village.
- Get E Line out of the central subway west of Boylston. Run under Tremont to the NEC and reconnect to E at Back Bay. New stops at Tufts Med/Bay Village and Berkeley.
- Piggyback Green Line tunnel to S Station under NEC when the N-S Link is constructed. Stops at Harrison Ave, South Station Bus Terminal, South Station.
- Connect with Silver Line tunnel at South Station. Run alongside busses to BCEC.
- Potential to continue line to South Boston.
- Potential to run off lines, battery powered through Ted Williams to Airport.
- Conversion of Silver Line to Dudley to Green Line, grade-separated or subway. Connecting at Boylston.
- Potential to continue from Dudley to Mattapan via Warren and Blue Hill.
- Possibility for revenue trip from C or D trains to Boston College via Reservoir/Cleveland Circle connections to B Line.
- Run Green Line stock from Airport to Chelsea via the RoW. Share Chelsea Bridge with traffic. Stops at Eastern Ave, Chelsea Station.
- Continue to Sullivan via Commuter Rail RoW. Possibility of serving future casino site. Two stops in Everett.
- Continue through the train yard to Grand Junction RR, run across Charles River and join the B Line back towards Kenmore. New stops at Twin City Plaza, East Cambridge, Kendall Sq, MIT, Cambridgeport.
- New routes allow for multiple forms of rerouting and additional branching along the Green Line. Great potential for growth.
- Branch off the D line to serve Needham along existing RoW.
Beyond these expansions, I'd advocate a crosstown Red Line Mass Ave bypass between Central Sq and the existing JFK/UMass. The Number 1 bus does not adequate to serve that corridor, and the Mass Ave corridor has such heavy volume that a radical reworking of space allocation may be impractical. The cost of such a line (including Mass Ave cut/cover, Charles River crossing, and navigating Back Bay fill that could require a deep bore) would be enormous, but if Beacon Hill ever gets the Ts financial house in order, it would be worth studying.