Slightly Crazy: let's imagine a future where the Downeaster runs on upgraded tracks that would allow service similar to Florida's Brigthline (90 to 110 mph service)
Would such a service need/want to be limited stop? Imagine cutting a deal that somehow required "Acela-like" stop spacing.
What would the stops be?
The only way you're doing 90 on more than trace *part* of the Downeaster is if it gets re-routed via the Eastern Route, because the Western is nowhere near straight enough for that. Trace on a map Revere-Portsmouth vs. Andover-Dover and it's screamingly obvious that geometry is not going to cooperate for that on the current routing out to the Maine border. While the trip would benefit from a Lowell Line speedup to 90 MPH where that is mostly feasible out to Wilmington, there's not a lot else you can do to push it above 60-79 MPH anywhere else. The Western is pretty much sitting right now at historical high speed limits.
If Portsmouth commuter rail restoration were to come first on the much more arrow-straight Eastern, you would be approximately 10 miles shy of the Eastern's old bend-back to the Western. The active stretch of Newington Branch bending sharply west of downtown Portsmouth to Bloody Point at the Piscataqua River covers 4 miles of that gap and is mercifully straight. That's the replacement for the old mainline from Kittery which isn't a good option because it ran too close to the side of the road on ME 236 to work all that well today. From the Newington end-of-track the NH 16 expressway cannibalized 5 miles of ROW to Dover when it was originally constructed, with the ROW reappearing for the last mile into Dover station at the Exit 7 offramps. You would have to reconstruct 16 from the Bloody Point bridge to fit in a new rail line on the side, but it's a fairly wide-buffered expressway and NHDOT will inevitably want to add-a-lane it. While the odds are slim of converging interests in backwards little NH giving an opening for project synergies, you could easily shotgun a highway reconstruction with a rail line reconnection that would feature similar speeds as the south-of-Portsmouth section. And it wouldn't cost an arm-or-leg to do in absolute terms...just probably too much for lowly NHDOT to consider in isolation.
Old vs. new routings meet at Dover, and stop selection changes from Anderson--Haverhill--Exeter--Durham--Dover over to Salem--Newburyport--Portsmouth--Dover. More or less a wash on ridership, though the downtowns it hits in Salem, Newburyport, and Portsmouth are much bigger destinations and there's a bit more of a true Seacoast focus with the routing. And you can definitely electrify all on the Eastern to here without problems while numerous clearance issues are going to make the Western in MA/NH the very last of the mainlines to get strung up. North of Dover the quantity and severity of overhead bridge restrictions is much lower, so you can try your luck with freight clearances under electrification in just Maine with a clearer (if still not altogether certain) cost ceiling for getting electrics to Portland. The bypassed NH stops on the Western can be then backfilled by NHDOT commuter rail service (almost certainly diesel) as a semi-express flavor of the Haverhill Line, reinstating B&M commuter service that ran until June 30, 1967 three years into the MBTA era. There were 10 commuter stops past Haverhill at the time: Atkinson, Plaistow, Newton Junction, Powwow River, East Kingston, Exeter, Newfields, Newmarket, Durham, Dover. Existing Exeter/Durham + Plaistow + a pick'em of 2-3 of the best of the rest probably suffices, while the others (esp. Atkinson, Powwow) were true zits from a bygone era. If Portsmouth CR schedules get brisk enough through the straight marshlands with the track upgrades to 90 MPH and electrification you could also potentially wrap Portsmouth CR and Dover CR to terminate at the same place in Dover at a large NHDOT layover and realign last-mile transit accordingly. Keep in mind as well, the Conway Branch forks off the Western just north of Dover station. That's used out to Ossippee by the huge Boston Sand & Gravel "DOBO" daily freight, but NHDOT has an archived study for rehabbing the derelict 13 miles of track to North Conway for low-speed passenger and freight service. The North Conway end of the branch is active for the hugely popular Conway Scenic RR, which runs excursion trains through the ex-Maine Central Mountain Division across interior NH. Should those 13 derelict miles get restored Conway Scenic would have direct access into Dover Station for excursion runs, which would be massive for NH's tourist economy. Conway Scenic stops right outside the entrance to Attatash Mountain, and when the branch was still intact and in decent enough shape through the very early-70's B&M used to make a mint running one-off North Station-North Conway ski specials during mid-winter. So there's also an angle to pursue in bullseyeing Dover as an all-things crossroads of New Hampshire transit.
That's probably the extent of it, as the Western is a little bit better-behaved curve-wise in Maine except for the big dive east to Old Orchard Beach from Saco, enough so that you're never going to see cost/benefit in analyzing reactivation of more of the Eastern. The Eastern has two other abandoned segments intact in ME: North Berwick-Biddeford and Saco-South Portland...with a little bit of residential encroachment in Scarborough blocking the old last 2 miles into S. Portland but where an early bail-out across a marsh trestle could rejoin the close-paralleling Western early without trouble. They're both quite straighter than the Western. The N. Berwick-Saco section misses Wells by a lot, trades a path through West Kennebunk where the Western stays 2 miles east near Kennebunk-proper...slight catchment demerits. Few miles in Saco are active for the Saco Industrial Track, and a relocation of Biddeford union station to the Eastern-Western junction and an I-95/195 park-and-ride in Saco-proper would do a bit better than the current route...which misses the highways as it divebombs towards Old Orchard Beach. Last abandoned segment misses OOB, but does stay centered on downtown Scarborough.
I can't see a compelling reason to change routings here even if there was infinite money to do it...which there certainly isn't in a state like Maine. The speeds aren't true game-changing levels better for all those abandoned track miles, and the catchments served on the alt route are par at best...and probably a smidge worse with Wells and Old Orchard Beach not being anywhere in the picture. So the only major pivot really becomes maxing out the commuter-driven investment in Portsmouth service by cranking up speeds where geometry affords, taking in the partially active Newington Branch trackage, and finding some synergy for the 5 miles of multimodal infill along NH 16 to bullseye that Dover crossroads. After that, work the Western in ME for what it's worth. It may not get faster, but you can empty the curve-easing bag of tricks to zero out a few slow penalties for tangible gains. You'll need those time savings anyway if the ultimate endpoint of the Downeaster is going to be Bangor on much longer-haul schedule, and Portland-terminating
Northeast Regionals become a minority flavor post-NSRL. In the meantime, 90 MPH to Wilmington on the Lowell Line serves multiple masters in the nearer term. If/when NHDOT ever gets Concord commuter rail online it's slated to be an above-and-beyond express flavor to the Lowell Line, running all-local in NH and express Lowell-Anderson-North Station in MA to keep brisk time while MBTA all-stops locals draw their line at a Nashua terminus. You definitely punch a lot of Downeaster tickets and generate a lot more revenue for those Concord runs being able to slice Lowell-Anderson and/or Anderson-Somerville down to their geometric minimums on the schedule with track upgrades to Class 5/90 MPH. The DE probably doesn't have a paydirt in 2020 to initiate that yet by its lonesome, but by decade's end its margins might be good enough to push such an upgrade project along if there are corresponding stirrings in the Granite State about finally getting their Capitol Corridor CR show on the road.