It is very exciting to see this project looking like it will actually happen after 40-plus years of talk and studies. I love the 2:50 travel time from Scranton to New York, which would be about 20 minutes faster than the best historical schedules -- and those wound up only at Hoboken. I also love the goal of 110 mph running along the NJ cutoff, which is a wonderfully straight stretch that was an engineering marvel in its day.
But if we're going to spend the money to achieve all of that, I think it would make more sense to get a third train set and build the second layover track in Scranton, allowing for more than three round trips per day. Option D may be the most workable startup schedule, but another frequency or two would make the service a lot more useful and versatile. And someone is going to need to lean on NJT to adjust its commuter schedules to accommodate this service. In particular, having no NYC departure between 3 and 8 p.m. seems like a huge gap that will constrain ridership. There also will need to be more than one departure from Scranton before noon, and preferably more than one arrival at NYP before noon.
And definitely, as others have said, the Scranton trains should all be running via the Morristown route.