Blow up the commuter rail system as it currently stands. Anything inside 128 is covered by the current, expanded subway system
Blue line goes to Salem
Orange line get two spurs to the north. One goes to Wakefield and the other Woburn.
Orange line goes to to Readville (cut and cover tunnel from Forrest Hills down Hyde Park Ave) and Dedham to the south (cut and cover tunnel from Forrest Hills down Washington to Dedham center)
Red Line line goes to Lexington to the north
Red Line gets a new spur from Central Square all the way to Waltham - cut and cover under Western Ave and Arsenal Street and then route 20 to Waltham center
Red Line has a new spur that replaces the existing Fairmont line. However, it runs cut and cover under Blue Hill Ave to Mattapan Square
Green line to the south has a spur that runs to Needham down Highland Ave
Commuter rail has 10 lines - central tunnel between north and south station gets built.
All lines run cut and cover beneath existing highways and major state roads. No stops once the lines hit 128. Smaller trains, more frequent service. True high-speed service. Where possible, rail lines will run between north/south and east/west highway lanes.
Plymouth to Boston under route 3 and then 93 (summer service May to October, extended to the Cape)
Fall River to Boston under 24 and then 93
Providence to Boston under 95 and then 93 (this would have a spur down route 1 to service Gillette Stadium)
Franklin to Boston under 109 to 95 then the Pike
Worcester to Boston under the Pike
Fitchburg to Boston under route 2
Rockport to Boston under 128
Lowell to Boston under 3 to 95 to the Pike
Haverhill to Boston under 93
Newburyport to Boston under route 1
All of these are existing commuter rail lines, just re-aligned and either put completely in tunnels, or running between highway medians. The only way you're going to convince more people to take the commuter rail is to have more frequent service, faster and more reliable service. Trains during peak periods should run every 20 minutes. For Amtrak, would removing MBTA trains from the lines benefit them?
So, some of those CR re-reroutes are actively worse than existing routings (sending Providence via 93 instead of SW Corridor is worse, Rockport via 128 instead of Rt 1 makes no sense unless you're going Rt 1 then 128 and there's no median to speak of, Lowell via the Pike is basically a middle finger to that whole routing). The idea of using highway medians isn't a bad idea, per se, but using them to the exclusion of anything else is crazy. The NH main I'm pretty sure can be quad-tracked to do CR and RT side-by-side, for example - no reason to route those trains via the damn Pike. Eastern Route up to Salem is 4-trackable at least to Lynn as well, if not Salem, so no need to reinvent that wheel either. Your pitch is Crazy enough just by extending all the RT termini to 128.
My concern is where you're branching all of these RT lines.
ORANGE NORTH: Where the hell are you branching Orange to send it to Woburn? Are you trying to use the NH Main to get up there? If so... are you branching at North Station? Because that's a great way to screw over transferring pax at Sullivan and Malden Center, since you can only pump so many trains into the Downtown pipe.
RED NORTH: Branching Red before Harvard is big-oops territory, because again you're whacking frequencies to a major bus terminal that is a major bus terminal because it's a major destination in and of itself. Red's already stupid overcrowded downtown anyway (in non-COVID times), this only worsens the issue. No argument with extending Red to Lexington, but... go with god on that one lol.
RED SOUTH: So we're branching at... South Station presumably to eat Fairmount? Interesting choice but alright. The main bus terminals are already on branches so that's not so terrible (though it's still a net loss and not one I'd like to see at all). But of course, now we've got three southern branches, and a whole bunch of questions on how to manage that balancing, considering that the existing Ashmont/Braintree branching can feel pretty wobbly at times. Also, why not simply have Red eat the MHSL to get to Mattapan instead? I know the aim is to get Fairmount off of CR and onto RT, but there's got to be a better way of covering Dorchester than this.
GREEN: This is fine, except for where it seems other plans (Orange to Woburn) might be overwriting things that are in the middle of being built, such as GLX (which runs up the NH Main).
EDIT because I completely forgot about the other Orange branching.
ORANGE SOUTH: Branching at Forest Hills isn't actually a death sentence, but I think going to Dedham via Washington misses the demand that is actually in the area, which has a stronger orientation to Belgrade Ave and Centre St. If you're going real crazy, find a way to re-acquire the Belle Ave ROW or tunnel under the houses and proceed to the Dedham Mall that way.