Why would Amtrak want to route their trains through the N/S Link? The proposal for Acela to stop at Grand Central was dropped in the latest revision of their 2040 Vision, so why is Boston a deserving market for 3 stops when New York City will have to deal with one? The most realistic vision for the short term, assuming that the tunnel and underground concourse can be expanded if the need arises, is this:
(1) 2 trains per hour on the Downeaster
(2) no more than 2 on the Portsmouth line
(3) maximum of 2 to Vermont and (potentially) on to Montreal
As for the commuter rail and regional rail routing to North Station, this just seems like an expensive solution to the problem of South Station at maximum capacity. There was a proposal on the docket until recently to relocate the Post Office so that additional tracks can be added, which would add all of the needed tracks to solve the capacity issue. I must say that I didn't like the initial renderings for the expansion, but that can be changed. I don't see how a N/S rail link would be a more elegant solution to the capacity issue than the South Station expansion.
The Acela and the Regional are two completely different animals with two completely different goals and priorities. I believe Amtrak still wants to stop their Regionals at both stations, and will likely want to stop Regionals at all three stations in Boston. The Acela, however, takes a huge penalty every time it needs to stop or slow down, and so there's emphasis placed on making sure it does that as few times as Amtrak can possibly get away with.
Any Acela train that would skip Back Bay in the future has to stop or originate from North Station for the Orange Line link - perhaps half of the Acelas would do this.
Another thing you're forgetting is that the identity of a train is not static - the entire train could empty out at North Station and pick up some southbound commuters, then continue on to South Station as a different train. Or vice versa. Mark from Melrose doesn't need to be commuting to Mansfield for that to be worth doing.
Finally, you mention the South Station Expansion Project, which is just about the furthest thing from an elegant solution you can get. No matter how many extra tracks we can tack on to the side of South Station, it's a band-aid capacity solution at best, and eats up far more space than simply building down would. Make no mistake, the expansion would require an overhaul of the station itself as well, and probably a more expensive one in the end. I'd bet we'd hit the capacity limit of the new tracks sooner than anticipated, as well, considering that the real reason we need an expansion - that being we are out of room in the yards connected to South Station - isn't really solved by just creating more platforms for out-of-service trains to get jammed up on.
Conversely, allowing those trains to use the yards connected to North Station, or even better, interlining those trains so that an out-of-service Stoughton Line train can continue on to Haverill instead, solves the problem more elegantly - and more permanently.
If you built a North - South Tunnel you could run Amtrak trains up to Portland and Concord which would free up capacity. Most of the people who use I-93 go trough Boston so there seems to be a decent demand already for a North - South Link. The New Haven - Hartford - Springfield - Brattleboro corridor will never use the Boston Network thats a seperate project. The Capital Corridor , Downeastern Extensions and Portsmouth line would greatly benefit from a North - South tunnel. Unlike in this region , Boston system is either electric or diesel which means you don't need to buy different trains other then dual or one power source....
I was wondering when you'd show up!
I'm talking about the New Haven - Hartford - Springfield - Worcester corridor, which is different from the Vermonter corridor you mention. In fairness, I had forgotten that the Vermonter was staying on its existing corridor south of Springfield, so between the Vermonter and the Inlander Regionals, the New Haven - Hartford - Springfield line is well covered.
Fine, but it seems like an expensive STATE-FUNDED project benefiting mainly people further down the NEC. If, instead of bothering with multiple portals and a complete redesign of the way that the station works, a single rapid transit portal to the Fairmount was built and terminal tracks built at South Station, that would do the job by letting Acela riders have a pretty easy transfer to Vermont, New Hampshire and Maine.
So basically we want a multibillion dollar tunnel and underground platform complex, all so that Mark from Melrose and Suzy from Swampscott can ride the train to their financial district offices without risking rubbing elbows with any unsavory characters on the subway? I don't think so.
Huh. So the real beneficiaries of the project are commuters coming in from the north, and intercity travelers coming in from the south, which means that a lot of people on both sides of the tunnel are benefiting! Glad we established that.