3. The military plot just feel so half-baked it's hard to suspend belief. They couldn't think of a better reason to have Pratt training raptors, or to get them on the island?
That is not why he was brought in. He rejected the militarization of his raptors, as did most of the board of directors. I suspect he trained naval dolphins or somesuch. No no. He was brought in to solve one of the problems with raptor behavior from the first movie (evident in the movies and the books). They were basically unsocialized. He socialized them. He imprinted on them at birth as pack alpha, kept them from killing eachother, and then did their social enrichment/play by way of target training and drilling. Zoos use that sort of training to keep their animals from getting bored and to make them more manageable when they need to be shifted for medical checkups and the like. Even Komodo Dragons get target trained so they associated a white target with food and can be lured and decoyed away from zoo personnel, and to remove the human=food association. It works so well with Komodo Dragons that they recognize their trainers and like being petted, because they no longer look at their trainer and see a possible lunch.
The Ingen Douche just read his reports and saw what he wanted to see. Just like management types the world over. Which is where the metacommentary on corporate culture comes in.
The military application subplot was really well done, actually. You just have to think about it a bit, and connect some logical dots.
1) Bossman does not know shit about biology. Unlike Hammond, he is a visionary, not a micromanager. He does not actually know the operational details of his own park.
2) The modifications made to a lot of the dinosaurs make no sense. Being featherless makes sense. It pisses me off, but it makes sense. They want their dinosaurs to conform to the mental image people have of dinosaurs. I suppose I just need to popularize the image of feathered T-Rex and the Raptor Death Turkeys. Anyway, using swaths of cuttlefish genome large enough to give iRex chromatophores in order to ostensibly give it tolerance to high growth rates (and high growth rates make sense for a park attraction that operates on quarterly profits) makes no sense. Unless it was intentional. The same goes with using raptor DNA for unspecified reasons that gave it increased intellect and capacity for communication down to suitable vocal apparati, and the ability to change body temp so not show up on thermal imaging.
Wu knows better than to just randomly split in genome sequences. Been there, done that. So it only makes sense if he did so intentionally.
3) Wu's answers were quick and specific when confronted about iRex's aberrant capabilities by Bossman. What is more important, operations personnel were not informed about the capabilities of the iRex, to the point that they took insufficient precaution when dealing with it. Which means Wu knew, and did not tell anyone else.
4) Ingen Douche came in during the disaster and confiscated the embryos of specimens that he did not want the outside world and corporate oversight finding out about. Experimental weapons projects obviously. More than iRex (possibly including the evil mutant Dimorphodon as well).
5) When Wu was being evacuated, he wanted assurances that "the deal was intact".
Conclusion) Wu and Ingen Douche (I am not dignifying DeNafrio with his characters name) had a secret deal. Wu engineers dinosaurs with obvious military applications for Ingen (technically, he is still an Ingen employee, and they are still bitter about being bought out) in exchange for a golden parachute. Wu uses the corporate desire for "bigger teeth" as a cover for this project.
4. Remember how in the first Jurassic Park, there was a tiny aside to Gennaro early on from the Ore Digger Guy that Hammond couldn't meet him because his daughter was going through a divorce and he wanted to be with her? Think it would have added anything to the movie if it had been expanded, and been brought up with Tim and Lex? Nope. Same thing with basically everything that happens with the brothers before they get on the island.
Are you seriously complaining that the movie shows instead of tells? "Family" vacation without the parents, the snap between mom and dad when the kids first leave, the younger kids general behavior (which makes perfect sense once he mentions that he figured out his parents were divorcing and you realize he was trying to put everything out of his head and have a good time, but was was having trouble coping), the mom's emotional ups and downs that, from other character interactions, dont seem normal for her. The phone call from a law office where there is obvious divorce mediation going on.
What do you want a big fanfare? Do you want someone to be like "Behold! The parents are divorcing and carted the kids off to jurassic world to shelter them from divorce mediation!"?