They can do that in FJ because the vehicles are actually individual cars and not connected to each other - they basically drive themselves around the track - more like Toy Story Mania.Outside of track and overall systems upgrades, something I'd like to see for the ride system is asynchronous loading for ADA/Wheelchair guests.
The slowdown that occurs with any Omnimover attraction detracts from the guest experience.
I don't know of any tech like this for classic omnimovers.
Simulated Omnimovers (where the ride vehicles are not directly connected but still operate in a chain) like Forbidden Journey accomplish this well, with separate load/unload without a conveyer for ADA guests.
With Martin's post about WDI looking into the ride system for this attraction, a simulated Omnimover like that would be useful, and quite interesting.
Not sure how it'd work with the steep slopes of SSE. But I'm not a mechanical engineer