While it would be great to have level-boarding bilevels for LD trains, it's not going to happen any time soon, if at all.
#1 - First and foremost, as all or nearly all stations west of Chicago have low level platforms only. There would be at least a 5 year overlap from when the first high platform bilevels debut and all stations have high level boarding. That assumes Amtrak has the money to BOTH build new cars AND upgrade stations at the same time! Good luck with that! During the overlap, all stations will have to be able to handle both low- and high- level boarding until everything is done. Station dwell time will more than double during the overlap period as, perhaps, only 3-4 cars at a time would be at the right-height platform.
#2 - Car design - Take a look at the new bi-level cars on the way to California. They have BOTH low level AND high level doors! Cars on the South Shore (CSS&SB) out of Chicago have the same arrangement. Roughly 30% of the stations served by the South Shore (once off the electrified METRA line at Kensington) have high platforms. The rest are all low level. Assume that each entrance on each side 'consumes' 2 rows of seats or one roomette, thereby impacting saleable seats/rooms/revenue. One solution would be like LIRR and NJ Transit does...high level entry at car ends over the trucks with some seating then a couple stairs up or down to bi-level seating as all stations have high platforms. Additional entrances would have to be at the low level seating to accomodate low platforms for Amtrak. Articulated cars such as used by various light-rail operators have everything low level, only a couple inches above pavement level and inside steps up to the ends over the trucks. Maybe something like that would work.
One of the more fascinating solutions I found was the light rail system in Denver. Everything is low level boarding and passengers have to climb steps. However, there is a ramp up to high level at the 'front end' of the loading area designed for wheel chairs to go up. When the operator stops the car, he stops such that the entrance directly behind him is at the high platform. He/She then easily swings down a light weight platform over the car steps that is level with the ramp. The passenger rolls on, the platform swings up and is latched. The whole operation is less than 2 minutes! Perhaps that would work. The 'key' is that the operator stops with the ramp directly behind them. Try to spot a 10 car train from a locomotive cab and line it all up. Yes, Metro North and Amtrak do it daily on the New Haven line if track 3 or 4 (the outside tracks) are out of service and temporary walkways are used over the out-of-service track. But that is the same engineers/operators doing it several round trips PER DAY, not an engineer that does 2 round trips per week (10-12 hrs each way). If my experience riding Amtrak from the Windsor Locks CT station with it's 20 foot long low level platform is any measure, at least 3 engineers consistently overshoot and have to back up to spot the doors from adjacent Amfleet I cars on the platform!
#3 - The idea of being able to pass from car to car at the lower level such as bilevel METRA cars in Chicago requires that the entire lower level is above the trucks. Because of that, the lower aisle 'gallery' is actually a foot or so above the floor of the upper level and headroom on lower level seating is such that it is impossible for an adult to stand fully upright from the seated position. So...the only way to provide 'reasonable' headroom on both levels is to increase the height of the cars. I don't know off the top of my head how high Superliners are above the rail, but I do know that double stack containers are 20 feet 2 inches. So there should be a couple inches available for increased height.
#4 - Another issue is where to put all the 'mechanicals' for the car...HVAC, lighting controls, brake valves and reservoir(s), and even restrooms. On Superliners, most of that is tucked underneath the stairs and some above the trucks. Where will all THAT be put for ease of access from inside as well as from outside for maintenance?
Maybe the solution would be to build a 'Super Train' like the NBC show maybe 35 years ago on TV. The cars were extra wide that on what appeared to be a double track 'standard' railroad the cars spanned the outer rails of each track making them maybe 25 feet wide, perhaps?