When designing the original Star Tours, the imagineers spent a lot of time figuring out which motions can be replicated in a simulator effectively, as well as making sure what it feels like you're doing lines up perfectly with the screen.
Oftentimes, motion sickness on simulators is caused when the image is out of sync from what you're feeling.
The new Star Tours, while fun, plays much more like a hastily put together video game- not to mention the ill effects 3D causes + the age of the simulators.
I also wonder if the new Star Tours being entirely computer generated has ill effects- since instead of watching something real and substantive, we're watching computer generated images that while convincing, often don't behave like a real object would.