For commonality you could just settle on one design (single level). The Venture, which is being added to the system on various regionals (including the plans for the NEC) would be a great starting point.
For the ADA issue, you could have a "core" on each LD train of a lounge / observation car, a diner, and an ADA accessible sleeper. Then add coaches and sleepers to the core. The only problem you would have is with the EB and the LSL which split.
How does Amtrak crew assignments work now? Does each Viewliner have an attendant? Losing that one roomette to the double bathroom module makes it rather inefficient compared to a Superliner if that's the case.
Maybe Amtrak should go with semi-permanent open-vestibule sleeper couple pairs?. That way one attendant can take car of two sleeper cars. And could a "drawbar/open vestibule pair" be considered one car for ADA terminology? How about two piece articulated open vestibule cars attached on one truck? Could that be considered one car requiring one ADA room?
Using coupled pairs of coaches and sleepers may make a big difference in efficiency and may justify going all single level. Although I do like the Superliners, the Viewliner sleepers have a much better room design with a more open comfortable feel.
As far as the "core" goes. That again could be a coupled pair with a lounge and diner semi-permanently attached. However I think you have to consider that the Viewliner diner is just too small to satisfy the needs of a full LD train. Amtrak's wish of going to a single "food service" car with the Viewliner is just ridiculous.
You have to think outside of the box here and this just might be the place you go bi-level. A typical bi-level NEC Plate car could have a full width kitchen on the bottom level and seating on the top level in the "dome" and also at both vestibule ends (with an ADA table at one end for coach passengers and one at the other end for sleeper passengers). Maybe the car could be used as a lounge when not serving meals or even better a 24-hour "bistro" for light snacks and drinks around the clock.
If business is really good, Amtrak could couple two of these together and have separate diner and lounge cars. Two of these on the LSL and EB would work out just fine. Now add a baggage dorm of course to max out the revenue numbers and you got a pretty efficient fleet.
P.S. I do have to say . . . . PLEASE Amtrak, whatever you decide, make sure that the seats can rotate forward on any new LD train!