So I am a little lost in this multi-page thread (which I don't like), but last I heard Ethan Allen Express (EAE) comes into Rutland, makes station stop, and then does a reverse move to head up to Burlington,VT. Yes, it's the "Palmer Junction" debacle, but over less time/mileage to final terminal of Burlington. Train would likely reduce speed through Middlebury, but that's expected.
Unfortunately I don't think there us enough room to build a direct connection from Rutland right up to Burlington that would avoid a reverse move. But the Vermonter no longer operates with two cab cars so give them to the EAE. This train is still popular with a business class car though.
And I would still try to schedule the EAE so it runs as late as possible from NYC to Burlington on Friday, with equal return schedule on Sunday......A 4 pm departure out of NYC would be great, for example, with arrival I to Burlington at 11:45 pm. Amtrak needs to truly run it as an Express with limited stops between NYP and Albany. This will help keep travel time down and ensure Vermont is getting it's money's worth and not be a combined corridor and once a day long distance train north of Albany. Perhaps a local at 3:30 pm (or train to Niagara Falls), then the EAE at 4 pm, and bump the Lake Shore Limited to 4:30 pm out of NYC - a slot it used to have for years!!!!