I keep procrastinating on finishing my proposal for the Rhode Island Rail (NOT operated by MBTA/MBCR) and have not drawn all of the lines, otherwise I would help with this.
I know that there's no commuter rail between New London and Wickford Junction (and with no Amtrak at Wickford or TF Green, you're effectively forced off Commuter Rail at Providence), but where's the other gap on the NEC?
Newark, Delaware (southern end of SEPTA territory) to Perryville, Maryland (northern end of MARC territory) is the other gap. A little wider off-peak and weekends because SEPTA doesn't run all the way to Newark/Univ. of Delaware except rush hour. Gap's about 20 miles total. MARC has a proposal to extend to Newark specifically for the SEPTA transfer revenue, so that one's not going to last too much longer.
The RI one will be filled, but by South County Commuter Rail running from Pawtucket to Westerly, and Shore Line east extending from New London to Westerly. CDOT has it on its SLE service plan that they are 100% going to Westerly the second RIDOT gets there. There's a layover yard at the station leftover from the
old Conrail Providence-Westerly commuter rail that lasted until 1979, so both services would be able to layover and turnback there. The station's also due to be rebuilt by Amtrak for ADA high platforms and 3 tracks. For CDOT it's a natural because Westerly is only 150 ft. across the state line and as much Stonington, CT's stop as it is Westerly's. And they can't currently go past New London to the existing Mystic stop (with all the tourist revenue from the Seaport and Aquarium) because there's no turnback spot that wouldn't totally screw with Amtrak schedules. So it's a no-build proposition for CT and in-district gap filler to get SLE to the border.
Next step for the Providence Line is extending to Kingston, because several Wickford trains will need to deadhead to Kingston turnback to avoid fouling Amtrak schedules. It's only when there's a schedule gap that they can turn directly at the Wickford platform. So all crews are being trained to Kingston, and they'll add as a revenue stop later. Amtrak is starting heavy construction on it for ADA high platforms and triple-track, so it's going to be in temporary torn-up condition for the next 18-24 months. That's why it's not on the table quite yet. At some point after RIDOT has weaned itself onto its own service and the Pawtucket, Cranston, and Davisville intermediate stops get built it's going to split off into its own Pawtucket-Westerly service. It's just too much for the Providence Line to go that far out-of-market. The T will really want to firm up its district borders and terminate it at T.F. Green once South County's running on its own legs. This is doable for the T right now, but the expansion of the Providence schedule that'll come after South Station's expansion hits a glass ceiling when they have to run that far south of Providence where only scant number of people are commuting to Boston.
Ultimately, better service is going to be MUCH more frequent Providence Line service turning at Providence or T.F. Green but no further, and a full-blown Pawtucket-Westerly schedule in-state. Since RIDOT will be "graduating" to some degree from the MBTA when it launches its own service, it's quite likely they're just going to keep on using the T's fare collection system to avoid the redundancy of starting fresh. At that point...one Charlie on one transfer gets you to Westerly. Which ain't bad at all when you figure how frequent these trains are going to be 10 years down the line.
And, yes, I bet MARC has filled the last gap by then, so by 2020-2022 (at latest...RIDOT is for-reals about this)...MBTA --> RIDOT --> SLE --> Metro North --> NJ Transit --> SEPTA --> MARC --> Virginia Railway Express gets you from South Station to Fredericksburg, VA via NYC and D.C. in one very very long all-day commute without once seeing the inside of an Amtrak train.