But trains like the Pennsy are not good for intermediate stops because they take a long time to stop, unload, load, and get running. Trains are better utilized for express services while buses serve the little towns. On this route that seems reversed, IMO a major failure of the transport system.
You are wrong on this one.
Trains like the Pennsylvanian are heavily dependent on intermediate stops. The time lost for a stop on 79 mph territory is about 3 minutes for acceleration (and deceleration; though my high school physics teacher hated the term deceleration and preferred "negative acceleration" instead; but that's neither here nor there), plus whatever your dwell time is. When the speed past the station is lower, the time lost is even less.
The revenue lost from the slightly longer trip for through passengers is often far outweighed by the revenue gained from making the extra stop.
The reason the Pennsylvanian is a relatively slow train is because it winds its way through the mountains, not because it stops to pick up passengers. Eliminating the stops would still make the Pennsylvanian a slower train than driving, but now it would lose even more money in doing so.
Even the Acela Super Express concept from the early 2000s failed, because the money earned from intermediate stops exceeded the value of the time savings from skipping them. If the fastest train on the continent, through the most densely populated region with extremely heavy business (time-sensitive) traffic makes more with additional stops, then definitely the Pennsylvanian would do so.