The NYNE right of way was bulldozed between Newtown and Waterbury to make way for I-84, so there's currently nothing connecting the existing Metro North non-passenger Beacon Line from Brewster-Newtown with the Pan Am Highland Line Waterbury-New Britain. It would be extremely expensive to stuff it on the I-84 grading because it's dense settlement and uneven terrain, and they'd have to tunnel through almost a mile of downtown Bristol, CT to eliminate a hairpin curve. Throw into that all the Westchester County NIMBY's and I think Plans B thru Q are going to have to be studied for the western routing with groundbreaking in the 24th century. But Metro North is 4-track to New Haven. Using the Springfield Line via New Haven should be workable if they do due diligence on the second NYC tunnels and a bunch of curve straightenings NYC-DC that have been on the planning books since...oh...1983 thereabouts. The 2-track shoreline New Haven to RI is the one that's unexpandable 2-track with all the crazy slow curves.
East of Hartford is easier because there's multiple ROW options and multiple fully intact landbanked ROW's, ability to open service in stages and still get to the end destination, and much lower density. I kind of like this combo as a first phase:
-- Build the long-needed, oft-thwarted I-384 expressway extension to Willimantic. The Feds have repeatedly offered, then un-offered, fast-tracking for this because it's so critical to mitigate the "Suicide 6" congestion/deathtrap, but everyone's been at loggerheads on a routing. Get it done already...this isn't optional long-term. Last design before the circa-'05 kibbosh was a greenway with 100+ ft. forested median separating carriageways. Prebuild a 3-track rail grading onto the highway construction with buried conduit piping for RR utilities. And leave it empty, waiting, and paid for by asphalt pork.
-- Springfield Line + active Manchester Secondary (ex-NYNE) to Buckland Hills Mall. Fairly straight, Manchester Sec. doesn't have any tough grade crossings to eliminate. Overpass the I-84/I-291/I-384 ramps maze and slide onto the existing I-384 median. It's wide here, and the highway's a ridiculously overbuilt 8 lanes so they could take the left lanes of 384 if they still want a large grass buffer.
-- Slide onto prebuilt ROW where the highway extension starts. Now you've got 160 MPH to Willimantic, as opposed to trying to restore the old NYNE ROW which is so curvy through Bolton Notch you'd be hard pressed to hit 45 in some spots. Plus it keeps the area trail network intact, and the highway will have fought and vanquished every NIMBY battle on the routing. 3-track ROW mitigates freight, because NECR in Willimantic needs to use this line to interchange with CSOR in Hartford (they're both owned by the same parent company).
-- Slide off the highway in Willimantic where it meets the old ROW at the junction with the NECR mainline. Slow-speed connections southeast to New London and Mohegan Sun. CDOT commuter rail can end here, and can use the 384 routing before any other segments are built.
-- Air Line alignment, Willimantic-Putnam. If they can mitigate the East Coast Greenway trail displacement, this is the all-landbanked former high(er) speed route to Boston. Probably 125+ MPH in most parts...no freight allowed.
-- P&W mainline Putnam-Worcester. Choosing this over the full Air Line to Boston for the regional hub connection in Worcester (MBTA, RIDOT Providence-Worcester, Amtrak to Albany & points west, continuing Boston-bypass service north via Concord, Lowell, Portland). Straight route, passing sidings can mitigate the considerable freight co-mingling. If they can keep it 80+ MPH sustained with maybe a couple 100 MPH straightaways, that's better than good enough.
-- Worcester Line to Boston. Worcester hub means commuter rail will probably be electrified before then, so if it's spruced up to Metro North New Haven Line like speeds and uses all of the ROW's former 3-track width (Worcester-128) it should be able to handle every passenger train thrown at it. All remaining freight except for Worcester-Westborough Auto Yard shuttles can be diverted onto detours (Boston/Framingham via P&W to Blackstone + restored segment of Franklin Line). Better first option than the full Air Line on capacity because of the 3-tracking and fact that it doesn't slam head-first into the overstuffed NEC at Readville.
That's immediately faster than the shoreline, maxes all of the existing lines that can get a bump to 100+ MPH speeds, and folds in a large connecting piece of true HSR into a highway project to save money and NIMBY fighting. The only 100% fresh build not shared with an existing transit mode is the Air Line Willimantic-Putnam. Which is in the middle of nowhere and under legal protection for reactivation.
And of course you can add other things later and make it a sort of "Choose Your Adventure" route. The Putnam-Blackstone segment could very easily get second-phase restoration to peel some trains off via Franklin. I-384 could get extended further (but I wouldn't bet on it) to I-395 in Plainfield, where the ROW could diverge in the woods for 2 miles and meet up with the NYNE at Route 14 for a straightish near-HSR to Providence. Or, they could forget about the highway ever happening and just use the active (but curvy) Willimantic Branch to Plainfield to restore the NYNE at regular speed to Providence for a mainly CT-RI audience.
In fact, you'll probably have to do 2 out of the 3 inland "Choose Your Adventures" to ram through the traffic and political will to make the west NYC-HAR bypass ever happen.