(1) The Maple Leaf is sandbagged by the border crossing time. You could arguably add a stop to one of the other two Empire Service trains (or the LSL).
-Putnam County is served by Metro-North. There might be a case to add an Amtrak stop opposite Newburgh (though that would still be in the neighboring county), but I'm not sure whether even that is necessary given the MNRR coverage.
-Herkimer County is pretty thin, and it's between Utica and Amsterdam. You have three stations "in the neighborhood".
-Madison County is between Utica and Syracuse. I think Syracuse provides sufficient coverage.
-Cayuga and Wayne Counties are between Syracuse and Rochester. Again, the distance isn't that massive.
-Genesee County is between Rochester and Buffalo...but the Depew station is on that side of Buffalo.
-Chautauqua County is between Buffalo and Erie. On the one hand, I think there might be a case to add Dunkirk, NY. On the other hand? The LSL is the only station calling there and the hours would be atrocious, so I don't think there's much gain to be had here. If there were 2-3 daytime trains on this route I'd say it would be a good candidate for an add.
In general, those areas have a bunch of really small towns (<15000 folks) and are served by nearby city stations. Putnam is covered by MNRR.
From start to finish:
-Putnam probably has more rail service than it knows what to do with. Of course, since I have bad memories of having grown up there, don't blame me for not wanting an Amtrak stop there.
-Herkimer (the town in Herkimer County) had a New York Central stop until the advent of the Empire Service in 1967. If the DEIS/EIS process moves forward more, I'd argue in favor of adding a stop there.
-Madison County is served by Syracuse
-Wayne County is home to Lyons, which was a Central stop for years. ESPA has been pushing for a stop there for years.
-Genesee is home to Batavia, which was probably one of the first communities to lose Amtrak service (early on in 1971!). The former NY Central station on Lehigh Avenue is still there, now a CSX maintenance base. Batavia probably didn't fare well because towards the end it had service in one direction and because of its layout was a poor place for a flag stop (elevated ROW). And since Geneseo (the SUNY school) is equidistance between both Rochester and Batavia,
-Dunkirk (Chautauqua County) would be a good stop-historic NY Central locale, near Fredonia. That said, you'd need a day train to make it work best.
Personally, NYS needs more of a network than it has now. Until Bruce Rauner's election in Illinois, they were in plans to reintroduce service to the Quad Cities (not completely on my preferred routing) and Rockford. I'd like to see Southern Tier service, and with the air service situation there, now would be the best time.