-The apparent genre confusion. The original Jurassic Park is essentially a horror film about dinosaurs with an adventurous atmosphere provided by John Williams' brilliant score. JW3 is directed as a knock-off of Daniel Craig era James Bond films for a good percentage of its runtime, and not even the good Daniel Craig Bond films. As a result, its primary selling point (dinosaurs) are kind of pushed aside for trite action sequences. But even if it were directed better, the shift in genre and narrative focus would still be jarring. It would be like if Toei decided to make the next Sailor Moon movie into a clone of Rocky Balboa. It could be the best Rocky clone ever made, but it would still be the worst installment of Sailor Moon.
-The misuse of legacy cast, wherein Alan Grant, Ellie Sattler, and Ian Malcolm just sort of stumble about like chickens with their heads cut off for most of the movie, which in many respects was just slightly out of character.
-The lack of any real statement on scientific progress or advancement.
-The stupid clone subplot that goes absolutely nowhere and is based on a philosophical pondering that literally no one can relate to or was ever asking in the first place.
-The horrendous editing and green screening.
-The extremely drab orchestral score.
-The fact that its central thesis (as established in the previous movie, all promotional material leading up to the movie's eventual release, and then recounted in the first five minutes of JW3) of a world where dinosaurs and modern day animals and humans are forced to interact is very quickly dropped and then hastily wrapped up at the end, where they decide that actually everyone lives happily ever after in the end. If you're going to advertise a movie so heavily around a specific key element, then it would probably be to your service to, you know, have that key element in the story.
-The runtime is too long, though this isn't a criticism unique to JW3, really. I've grown rather tired of three hours being a standard movie length. Screenwriters haven't used the additional time to flesh out the characters and story, just to pad it out for longer periods of time.
-The retcons and continuity issues between films, though I'm going to be honest that I can't be bothered to care too much about that given the plethora of more serious structural issues with the film's plot, poor pacing, and characters.