TMNT and JP seem to be very different games. I haven't played TMNT but it seems the progression seems less clear than something with linear progression like JP. The shots on TMNT seem to be a bit easier, but again I haven't played. The common complaint with JP is you can't just flail balls around to progress. JP is much more a shooter even in multiball. Personally that makes me enjoy JP and I feel like it's making me a better player.
With that said I can't wait to play TMNT and I think it would be a nice compliment to JP.