Certainly ridership and demand is way higher than the Metroliner era and I imagine more trains runs today than back then. Once the Avelia Liberty equipment there might be the enough trains to justify the trains for the occasional "Big 3" (NYP-PHL-WAS) only train. If that train makes only one stop between Penn Station and Union Station instead of 5 or 6, how much time is saved? Certainly you should be able to fill a train with NYP-PHL, NYP-WAS, and PHL-WAS passengers today.
This was also in the Acela era. They attempted to run an express train between NYP-PHL-WAS. Then, to stimulate ridership, they added MET...which helped. The truth is, downtown to downtown is not the market some of you think it is.
The only benefit is these train ran ahead of previously packed trains. This loosened up space for the not downtown to downtown travel on the congested trains.
However, that is not the concept of this thread. Is a WAS-NYP-BOS train feasible? Sure. Would it be beneficial? Not really as it would also increase the razor thin margin for failures (and cancellations) in exchange for minimal benefit.
When the new trains come online, then we can have this conversation.
Then again, when they come online, you may not have much of a choice but to ride them.