Lets all be honest with ourselves again here. I don't mean to be a broken record, but this is NJ Transit. When was the last time they had a train skip a stop west of Summit that wasn't named Mt. Tabor? We're not talking about Metro North on this route like we are going to Port Jervis. Trains to High Bridge, Bay Head, Hackettstown all require many, many local stops along the way.
This whole thing is moot though because there is little hope of this line going past Andover in any of our lifetimes. Even the federal high speed rail money that was once given out across the country is all going away. Deficit cutting is now the name of the game both at the state and federal levels.
Jeff is right, though. The only way that this project could ever get off the ground would be from funding from a private company, and that will never happen.
I think it may be possible that NJ Transit might not be the perfect, infallible organization that most people assume it is.