Some thoughts from someone who may or may not know what she is talking about:
Assigning seats at the time of reservation could alleviate a lot of other problems too. In stations like WAS you have people lining up an hour before their departure time so they can be the first to board the train and get the best pick of seats. All the long, sprawling lines detract from the usability of the station. If all those people had their seats assigned in advance, they could spend most of that hour in the food court (or elsewhere in the station, or at home), then stroll onto the train 10-15 minutes before departure and take their seats.
On the long-distance trains, I appreciate the efforts taken to segregate passengers who will be disembarking at daytime versus nighttime stops. But surely that can be taken into account when you're offered your pick of seats (i.e., you can't choose from any seat on the train - just from those in the car designated for nighttime destinations, so the passengers in the daytime-destination car don't have to listen to you shuffling around to collect your stuff right before your stop).
If none of this would work for some reason, I wonder if Amtrak could keep separate inventories of window versus aisle seats, and sell them at different prices if necessary? The system is already set up to do that with upper and lower level seats, so it should be possible. That way, people who really want a view out the window don't have to stress out about whether they'll get one, and the people who just want to get where they're going may be able to save a few dollars.
If anyone recalls, they started this service with the Acela and passengers hated it. It also didn't work correctly. Different trains have different loading plans. Some of them are based upon the train size, service requirements, host requirements and station size. Some stations may need certain cars on the platform to accommodate baggage work. There may be a group getting on and they need the seats for late. They may want the person that is getting off first on the aisle because some people sleep like to relax during the day as well.
What works on one train may not work on another train because operating profiles are completely different.
To that end, they were supposedly working on some system that will do exactly what Johanna stated. It would show the consist, the car diagram, the seating chart, the direction of the seats etc. It is part of a massive overhaul of the operations system. Some of it has already been completed. It may help but I'm not in favor of charging people for window seats, forward facing seats (etc.)