The ride layout itself is different. There is this big aquarium scene when you first enter. The old ride just had dinosaurs moving around in it. Multiple boats could be there. Now there is an actual show. I am no expert, which you are not either.
But I am sure there are issues with the ride and I for one am happy they opened it. I rode it twice last night. Had no issues with the wait or the unloading.
But on JW, you are exiting a boat that is below the loading dock and you must step up. Transformers is high up and you step down. Much easier. Plus Transformers is 9 people per ride. JW is 25. Lot more people to get on and off.
Disneyland, MM, Knotts, Sea World all inflate their ride times. Nothing new here.