I owned a JP and sold it to a friend before I really spent any time on it. Just bought a NIB JP prem and really getting into it. I have owned an AIQ pro which I liked but traded.
As far as comparing the two, both games have amazing shot opportunities/ angles. Each game is designed extremely well , with a lot to shoot for with out seeming crowded or tight ( see Houdini). I think the difference is in the rules.
AIQ, is improved dramatically with a pin woofer sound system. The game gives you a lot of choice as far as modes and GEM placement. I can see why it is very popular from that stand point. The rules are pretty complicated for me. I tried to get through the written on line rules once ,but got a headache . I would play a game and have no idea why it was counting up bonus scores at the end of a ball. Needed to spend more time on the rules ,but got a chance to trade for a ST and took the trade. The game would be great for a really good player that can spend the time to get down the intricacies of the game. I will probably try to get a pre/LE down the road.
JP is also a plethora of great shots/angles. The rules are a little more straight forward, but detailed/complicated enough to keep one interested for a long time. It may be a bit more clunky when you are not hitting your shots. I am getting into it in a way that I have not with any other new game in recent memory. It will be a keeper next to my SW comic prem.
At this point I vote JP based on the easier but still complicated rules. I would have no hesitation getting an AIQ tho. It also is a great home game.