There's an argument in here somewhere that you don't necessarily through run all the lines because Greenbush and Fitchburg need a connection, but because all the lines should have a roughly equal demand to either terminate at North or South Station, and if they're all using the Link anyway why not through run them.
Of course, that's a disingenuous argument at best - but it's there.
The best option really is re-engineering South Station to be Central-esque Station, and having all your non-through-running trains terminate there. North Station would be 'demoted,' after a fashion, from terminal status.
For this to work, though, you really need 6 tracks in the Link - four going south and two going north, and I don't see room for a rapid transit option in that, except for a Fairmount-style rapid shuttle option.
I'd also want to study whether or not we can connect Springfield-Worcester to the Cape on some kind of revitalized Cape Codder or Inlander Amtrak routing, but that might be an exercise in futility.
The tunnel can fit a max of 4 tracks on the Artery footprint. Central Station was proposed for maybe 6(?), SS and NS 6-8 where the underground footprints could be wider and more level. They don't need anything stopping in the middle...CS would be an epic clog if they actually tried that, in addition to having the crippled platform.
Now, the reason why they can slice-and-dice it as half-RR and half-RT is that, unlike all the tunnels in NYC, these aren't 1-track-per-bore digs where you're fucked if a train breaks down in the tube. The Link would have everything side-by-side with frequent crossovers. It's not going to be rendered useless by a breakdown, and it's much easier to dispatch asynchronously with 2 crossover-able tracks going in the same direction if there's a schedule slot open with nothing heading in the opposite direction. That kind of dance happens every single hour through maximum-overlap spots on the NEC like Ruggles. Throw on top of that that the there's a hell of a lot less thru traffic potential north/south through Boston than NYC, and you can see that 4 tracks is actually a bit generous for capacity. I would just build it as 2 tracks + 2 empty berths to keep startup costs low, build as 1 thru NEC-to-NH Main shot with provisions for the extra portals...then figure out the sequence of add-ons 10 years, new studies, and new appropriations later. The rapid transit half would draw more riders in my opinion, but there's nothing stopping them from opting for 4 RR tracks and extra portals later (though if they don't combine the Fairmount + Old Colony into one I can never take this seriously). Emphasis later. You do have to build and crest demand, after all.
The monolith is either stupid or disingenous...there's at least 5 pieces (2 extra tracks, 3 extra portals, 1 extra station) that are in no way gonna make a difference for the tunnel's first dozen years of ramp-up operation. And they are ALL provisioned for, and ALL can be acted on individually. Just like nothing about South Coast FAIL requires it to be a monolith. Virtually every piece can be built separately and ramped up gradually. A straight NEC-to-NH Main build can handle Providence, Worcester, Lowell, Haverhill, Franklin, Needham, Stoughton/South Coast/Cape-via-Taunton-and-Middleboro, Newburyport, Rockport, and Fitchburg-via-Lowell traffic depending on extent of electrification and use of the same kinds of dual-mode locomotives that Amtrak/Metro North/NJ Transit use every day in NYC. The ONLY lines shut out from the base build are Fairmount (to Fairmount), Greenbush, Kingston/Plymouth, north-of-Middleboro, and east-of-Ayer. Consult the Blue Book...that is not very much ridership as a % of the system. And I think not even close to justifying the 2x'ing of the project cost to build the extra pieces. They've got more routing options on the base build than they'll know what to do with. It's stupid or disingenuous to serve it up as build all bling at once or it's not worth building at all.
