I don't see it as an inherent issue of the trackless ride system, but an issue with ride design. Attractions like MMRR and BatB are designed with an effort to try and "showcase" the trackless system by making the vehicles dance and show they can be synchronized and go on various paths. Most of that can only be accomplished with wide-open spaces. RotR works well because the attraction itself was the forefront and the vehicles are secondary to move you through the space. It was also able to showcase that the pairs of vehicles can be separated for a brief period of time without the need for large warehouse rooms.
I think 90% of MMRR's problems can be fixed with some simple adjustments:
1. Figure out a way to project onto the ceiling. It doesn't have to be perfect, but what you see in your peripheral makes a huge difference. The black above you takes you out.
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3. While at it, paint or project on the floors too.
2. Figure out a way to add more depth to the background images so they don't completely look like walls with projections on them.
3. Remove the pointless dance studio scene. It was clearly put there to showcase that the vehicles can do synchronized dancing. We already got that demonstration with Luigi's.
Not saying it's a terrible ride, but they could have tightened up some effects and story points to elevate it to the next level.