The principle problem that I have noticed with changing livery (and let us, please use that term rather than "paint") is the fact that rather than "paint", most livery schemes are vinyl stickers.
When Amtrak gets sick of one livery, they peel the stickers and put on new ones. But they don't do their best to clean where they've peeled - or maybe they do, and the stainless steel is brighter behind the residue. Regardless, when you see remnants of a previous livery, it completely destroys the aesthetics of the new one that has replaced it.
I would argue that the US is one of the last countries where their major long distance trains are still "rainbow". Not quite like the rainbow days of the 70's, but mismatched heights, paint, cross section shape, etc., are all a true shame to an otherwise fairly cool rail system.
Perhaps the only consist/livery in the Amtrak system that doesn't look "odd" in my own humble opinion is the completely unmodifiable Acela. But it's a waste of platform space with its two locos serving a mere 6 coaches.
1. All Superliner, Pac Surf, Talgos are pretty consistent most of the time. However, the P42 or F59PHI that hauls them are not the same height or paint scheme as the coaches. Worse when a green loco is set up with the "swoop" baggage car on the Talgos. The baggage car on the Superliner sets disrupt the flow between the loco and the Superliners. Medium height loco, single level baggage, two level superliner... Ick.
2. The NERs look pretty consistent. The locos are a bit tall for the rest of the consist. I still prefer weight distributed DMU/EMU's, but I know we can't expect that so long as we have to have these trains jump from diesel to electric systems.
3. The worst have got to be the ones we're talking about most in this thread - the Single Level sleeper trains. The Viewliners are almost the same height as the P42s. If there were ONLY Viewliners in a consist, and the livery was good, it would look fantastic. But I don't think there is any plan to replace the coaches with Viewliner shells - who needs 12' ceilings in coach?