The most likely rail rapid transit extensions are the Blue Line extensions discussed above, and some relatively easy/cheap projects:
- Orange Line to Roslindale: frees up a lot of buses, and can be done without major CR disruptions
- Green Line to Needham Heights: already studied, though it probably needs to wait for the Type 10s to increase subway capacity
- E Branch extension to Hyde Square: serves the part of the Arborway Line furthest from the Orange Line. Easy to do once Huntington Avenue rebuild adds accessible stops and maybe transit lanes.
- GLX part 2 (Route 16) and 3 (Porter): Somerville and Medford are going to keep pushing for these. The only tricky part is the tunnel at Porter; you might see a partial extension to Spring Hill in the interim.
- Green Line branch to Nubian: this would be pushing it on subway capacity, but Washington Street desperately needs reliable high-capacity transit.
After that, you start getting into projects that haven't been official proposals for a long time, or that were killed during planning. Orange to Roslindale + Green to Needham Junction is the most likely; Red to Arlington Heights, Orange to Reading, Blue to Kenmore, a rail Urban Ring, and some sort of SL or GL tunnel to South Station round out the usual suspects. All of them would be more expensive and require a lot more political will; I can't seen any of them happening before 2040 even in the most optimistic scenario.
Ultimately, a lot of the capacity you can wring out of the urban core in the next few decades is going to be buses. Dialing up the frequencies to acceptable levels (requires new garages), BRT projects like Columbus Avenue, etc. Blue Hill Avenue and the SL spurs to Everett, North Station, and Kendall are official near-term projects; medium-term, building out the rapid networks in Roxbury-Dorchester-Mattapan and Chelsea-Everett-Revere-Malden can do a lot of good.
Additionally, NSRL and commuter rail electrification will act almost as an additional core subway line. Getting 15-minute frequencies on the inside-128 portions of Worcester, Fitchburg, Fairmount, and Newburyport/Rockport will vastly increase the amount of the metro area with walk-up frequency, and the combined frequencies through the downtown section will be equivalent to a subway line.