I definitely prefer JP for many reasons.
First, the storyline is much more familiar and "reasonable" due to that, the storyline of Dinosaur is kinda iffy at best and quickly portrayed. I'm not a big fan of Dinosaur either because it's startlingly loud and rough, but for me it doesn't translate to fun. You're thrown into the action from the first minute and don't get a chance to rest until the end...that's basically what makes it the most scary ride at WDW (IMO)
JP has a slow build up of drama as you see things that start to happen and like a good storyline, builds up over time into more and more intense scenes until the major scary ending.