Yes, I know you didn't include some things due to the OP; however, I believe pointing these items out demonstrates how Disney has been becoming less friendly to the disabled community as of late.
I know many of these items are not required by ADA, but ADA guidelines should be viewed as minimum requirements, Disney has in the past gone above and beyond these standards and I would expect them to continue to provide that higher level of service, especially given the prices they expect people to pay. Yes, they can technically get away with meeting the minimum requirements, but this isn't in the spirit of how Disney has operated in the past and shouldn't be the way they work now. Instead they actually go lower than ADA standards in many cases (see current number of accessible spaces at the parking structure at Disneyland resort as a prime example, they technically don't have enough spaces at present and the ones that are available are as far away from the shuttles as is possible, making those that are disabled walk further than anyone else.
As for the Millennium Falcon, they could potentially create a ride vehicle and require transferring to a Disney wheelchair, obviously this would not work for everyone and isn't ideal, but it could work and limit the number of chairs they have to design for. But I can think of several systems that could indeed work, additionally like with other attractions they could offer an alternate experience as a choice as well, not sure that they will, but they could.
As for Navi Boats, exceptions can be made to needing the companion seat (see Buzz at Disneyland for example, last I checked its companion seat had been removed) on accessible vehicles when necessary. And as I said, the ramp wouldn't be on the boat, it would be outside the boat, similar to how wheelchairs load and unload from the Safari, the ramp would be external and it could be done, there might even be able to be enough room for a fold down companion seat. This really wouldn't be too hard to do, you get the wheelchair in first, then fold down a seat for the companion, again using a ramp from outside the boat. Now, it would not accommodate an
ECV, but a wheelchair, even a wide width one it could.
As for a bus ride, you must not live in an area with very many hills, how do you think
ECVs fair on public transit in cities like San Diego, San Francisco, etc.? Yes, it can be done from a technical standpoint, but as you say a separate stationary theater would have worked as well, which I suggested above as an option and again Disney in the past has done this and went out of their way to do so, the fact that they chose not to in this case shows the current attitude at Disney is not near as friendly to the disabled community as it used to be and I think that was the OP's original point.