At the risk of getting yelled at for bringing regionals into the discussion, I would agree with markhb on the topic of LD trains having limited stops. Not an end-to-end express, obviously, but take advantage of more regional situations to collect and distribute the LD trains. You already do so with some regionals that branch off of the LD routes, but within the LD routes themselves, using the LSL as an example, I agree that the Empire Service could operate as a collector to bring LSL riders from some of the smaller and closer stations on the route (particularly in the eastern end of the state where you have stations so close) and meet up with the LD routes. I understand in some cases you'd add new trains to the mix, but if we're looking pie-in-the-sky here, why not? It could also provide the opportunity to add some more small stations in between on other LD routes and keep the LD routes moving quickly.
Just as a purely hypothetical example, without being super familiar with the economics of the stations in between, but run a smaller train from Schenectady to Syracuse, stopping at all the stations in between, that would arrive at SYR about half an hour before the westbound LSL's scheduled arrival. This would be a "guaranteed connection" stop, meaning if by some fluke the LSL managed to pass the collector train, it would have to wait. Turn the collector train and wait for the eastbound LSL, and anyone destined for stations between Syracuse and Schenectady would switch trains in Syracuse. This way the LSL could run full speed ahead to Albany without making a bunch of smaller stops. You could do the same thing from Utica to Albany and vice-versa. It adds trains, it adds turns (or push-pull operation) but it definitely makes the LSL a "Limited" in the original sense of the term from the pre-consolidation railroads. Obviously this is just spitting out a thought, and more research would have to play into where and how you operate your collector/distributors.
The same could be done for other LD trains, maybe even the Maple Leaf between NYC and Buffalo. I'm not entirely familiar with the station spacing on trains out west, such as the Empire Builder, but you could probably do the same thing to speed that train up some, and also add some smaller stops in between, even if they become "flag stops" in a sense (only stopping if there are tickets purchased where that station is an origin or destination for that specific day).
I know this would also complicate some matters in that you'd start and end with empty-ish trains, and that would probably cause concern for some. But you don't offer amenities on these either, they're simply there to get you to a "limited" station for the LD train and inter-city travel within their territories.