As a theme park nerd, Dinosaur has always impressed me a lot more, even with the obvious cutbacks in the theming. Dinosaur uses a high tech, custom ride system, and, even though its the same as Indy, its still impressive. The story is also pretty decent, too. I've never felt that the setup and pre-show are cheesy like some people think.
The best thing about Dinosaur is how everything makes you feel like you are truly in the action, thanks to the ride vehicle and ride system.
Jurassic Park - I like the setup, and how the boat ride you are on is supposed to be a slow, educational tour like the jeeps in the original movie. But in the end, it feels like exactly what it is - a longer, taller "chute" ride with elaborate theming. You never really feel connected to the action at all, if that makes any sense. There is no intensity, unless waiting for the plunge makes you nervous.
The theming for JP, and well, almost all of Islands of Adventure, feels like the theming options you get in the Rollercoaster Tycoon games. You build a standard amusement park ride system, and you can place theming around the track to enhance the ride, but not as if the ride was designed to where that theming is part of the ride.