I was making this same choice and chose Jurassic Park. I spent hours on each game at this point. I also own a POTC and love JJP in general. My reasoning is based on:
1. My strong preference for the JP code. I wanted a mode based journey pin and/or a rule set that invests me in the theme somehow. Jurassic Park offers 3 separate pathways of modes (control room, TREX, and paddocks) + the rule set is thoughtful as to the theme (different dinosaurs have different behavior, as one small example) so it wins on that. Moreover, I like that each of those pathways has an associated mini-wizard mode so there is something to achieve at the end of it. It allows the depth of a journey while still allowing the breadth of many choices. Willy Wonka's code design falls flat for me as it feels like a lot is going on at the same time yet is not generally speaking a mode-based game nor do I feel invested in the theme as I play (the one exception would be the mini-wizard modes). Although Wonka does have all those mini-wizard modes, several of them are achieved through multiball success and I just don't care as much about that. It is just my preference, but I don't feel invested in that.
2. I would rather have the new story that JP tells than the mixed use of limited resources in a jumbled way that is presented in Wonka.
3. I hate the sounds on Wonka more than I dislike some sounds on JP (which are more likely to be replaced by someone in the community anyway).
4. I'm shocked to be saying this, but I prefer the mechs on JP Premium than Wonka LE. Never thought I'd pick a Stern over JJP in that regard but there you have it.
Other points:
-They both shoot great.
-love JP de Win, but I actually prefer animations on Jurassic Park over Wonka.
-Art is above average on both but neither sways me strongly compared to say Deadpool
-Wonka does have better lighting BUT there are way too many lights on at once such that they fight each other in my opinion.