Here is Adrian Herzog's master plan for Amtrak routes. I think it agrees with some of your desires.
Thanks. I am not familiar with Dr. Herzog, but I found someone posted some YouTubes of his lectures here: Dr Herzog explains Rail Passenger Matrix Theory Part 1
I admit I haven't studied the route maps adequately to fully digest his Matrix theory. I'm just pointing out what seems to be logical, regional routes that need to be connected.