Considering Dinosaur, well techincally the CTXRover vehicle, is the inspiration for my username, I may be a bit biased, but I think Dinosaur is a much better ride. Beyond the really cool T-rex animatronic at the end, the rest of JPRA's dinos look cheap and they move like they were cheap. I remember the first time I rode it looking over to my brother in surprise at how bad the first brontosauras (or whatever its name is ) looked. It looked and moved like a crane covered with Dino skin...and it still does. The rest of the dinos in JPRA also have very limited movement, if any at all. It could be the slow moving ride vehicles, but I've always thought the skins on them looked fake and rubbery....and many a times I've seen the dinos with their "skin" tearing at the seams.
In comparison, there are several dinos in Dinosaur that move with exceptional speed....particulary the first dino that pushes the tree over, the one dino that eats the other, the "long neck" and all three carnotauras encounters. Its probably the speed or lighting of the ride, but they look a lot more "real" to me.
For overall enjoyment, Dinosaur takes the top prize for me as well. Its quicker, more thrilling, scarier, and overall more exhilarting than JPRA. The JPRA has some nice theming in the first part of the ride, but once you enter the building, its pretty much a disappointment until the T-Rex scene.
Don't get me wrong, I think JPRA is a very good ride and always go on at least twice on my visits to IOA. I just thought Dinosaur was better fron the get-go. Could also be the fact that USH has a much better version of the JPRA in comparison to the IOA one as well.