Extending Orange and Indigo to a meeting point at Readville would be a great start. Extending one or both to RTE 128 (and a real Amtrak connection) even better--like New Carrollton. And electrifying Indigo best of all.
All would make it possible to re-balance the whole system between RTE 128 and South Station.
Only 2 things they have to do to get Fairmount extended to 128:
-- Do the Readville-Canton Jct. tri-tracking (128's outbound platform is already designed as an island for that third track). I would not be surprised if there's a small stimulus grant for that in the next year or two because it's cheap, fast, and does not require Track 3 to be wired up initially (it's for grade separation of CR from intercity). South of the station old Track 3 already exists for 1/2 mile as a repurposed freight turnout, so a portion of the construction would be straight rehab instead of all-new.
-- Reconfigure the Fairmount Line Readville platform so it's a 2-track island shifted about 200 ft. north of the current platform, before the switch:
http://goo.gl/maps/9gyJE. That way 2 trains can occupy it, and you can mix and match trains continuing on the NEC vs. trains using the Franklin (right now that platform's only accessible from the Franklin). Only reason they haven't done this already is because current Readville is ADA-accessible, and wasn't as high a priority as getting non-ADA dumps Morton St. and Uphams Corner upgraded. They want to do this when they can find the spare change. They need a 2-track platform to achieve the envisioned service levels non-awkwardly.
That's it. When service levels start to make 128 more congested, notice all that extra space on the easterly side and the extra underpass berth under 128:
http://goo.gl/maps/QQypS. That's room for a future 2-track turnout that Fairmount trains can use for themselves. At full build the station could support a total of 5 tracks (2 island platforms + 1 side), with that expansion turnout merging quickly back onto the main on either side.
No way you're getting an Orange Line extension down there. Amtrak's bringing back NEC Track 4 from Forest Hills to Readville so Franklin trains grade separate at the same spot Needham trains do. The Orange Line would've reduced it all to 2 tracks, which is a total nonstarter. Also, check the ridership projections in that OL extension option vs. the Rozzie-West Roxbury-128/Needham option...not even close. The Mt. Hope area is too much of a transit 'tweener'; Rozzie Sq. absolutely blows it out of the water on ridership and bus connections.
But even if you consider rapid transit on/along the Fairmount Line instead, there's no way you're getting >4 side-by-side tracks through
these wetlands. NEC Track 3 restoration is the single biggest congestion mitigator Amtrak has identified north of Providence. And they're probably going to need a continuous Track 4 to Canton Jct. as well in another 25 years, esp. if the Inland NEC goes via Providence instead of Worcester and doubles up the high-speed service on those MA miles. No way you're fitting 2 rapid transit tracks there and kneecapping NEC capacity...that's suicidal. I think dense Fairmount short-turns are the best solution.
Note: doesn't mean you can't go TO Readville with rapid transit. I've mentioned in other threads that all it takes is 1/2 mile of River St. subway or 2000 ft. of deep-bore under residential property lines to get the Red Line from Mattapan station to the portion of the Fairmount ROW that used to be 4-track from all the old freight sidings. Neither all that cheap nor Big Dig-level expensive, but you could go to Readville and then turn west to Dedham Ctr. on an erstwhile Ashmont train without touching a single track's worth of NEC or Fairmount capacity. Not saying it comes close to cracking the Top 5 most needed rapid transit extensions (you do, of course, have to get the RL trains replacing the trolleys first), but it's definitely engineering-feasible.