Throughout the film (and especially in its advertising), they play up "genetically modified dinosaurs" as something new, revolutionary, and dangerous. Dangerous it is, but not new or revolutionary. Chris Pratt's character, Owen, criticizes the new
I. rex as something "cooked up in that lab"; Bryce Dallas Howard's character, Claire, describes it to investors as bigger, better, faster, stronger in ways that nothing before has existed.
But near the middle of the film, Henry Wu (B.D. Wong, reprising his role from the first film) tells Simon Masrani (Irrfan Khan, playing a South Asian version of Mark Cuban) that all of this moralizing and hyping is nonsense. The dinosaurs in the park were always gene-spliced abominations. They had to introduce code to fill in the inevitable gaps in each DNA sequence; they had to introduce code to make the animals better-adapted to a modern environment. Wu points out that even the original favorites, like Rexy and the raptors, barely look like the original article at all - a nice way to account for the fact that the JP raptors are completely unlike any species of
Velociraptor that has ever existed.
Wu is cast in a sort of villain's role, but he's not
wrong in pointing this out. In fact, the conversation between Wu and Masrani mirrors one between Hammond and Wu in the original book. In the novel, Wu is trying to persuade Hammond to let him make more modifications to the animals: he wants them slower and more docile, because he fears that people will think that they're too fast to be real, too dangerous. That was, after all, the image of dinosaurs in the public mind back in the eighties: massive, lumbering titans, not quick and birdlike. Hammond ignores the suggestion and claims that the animals as they exist are real, and real was good enough. And Wu, just like in the film, insists that they are
not real, that they were always genetic abominations, and that any assertion otherwise is just willful ignorance.
I feel kind of proud for pointing this conversation out several months ago. (Apparently, the thread was baleeted.

) Trevorrow himself has used it as ammunition in Twitter arguments, which amuses me to no end: citing the chapters "Version 4.4" and "Tim" from the original book in arguing against misguided fans is just too funny.
Incidentally, Wu's motivations in the book were fundamentally about tinkering with the science, seeing what he could make, publishing, achieving academic immortality, and pushing the boundaries of genetics. He was also generally quite ignorant of the consequences of all that he did in a fairly monstrous way. Trevorrow, interestingly, pairs him up with Hoskins (Vincent D'Onofrio), another InGen manager who is interested in the military applications of these de-extincted biologicals; that Wu would effectively sanction the use of his work for war continues another idea thread in Crichton's book. Ian Malcolm, Wu's primary critic in the book, speculates about the nature of genetic power in his many drug-induced philosophical rants, and suggests that it will be easily adapted to use as a weapon in kits for dictators and terrorists. And indeed, Wu and his embryos get bundled off to an undisclosed location late in the film on Hoskins' orders, in an instance of fairly obvious sequel-bait.
There are, of course, many other parallels between the film and the first book.
Zach and Grey escape from
I. rex by going down a waterfall, in a scene vaguely reminiscent of Tim, Lex, and Grant's use of the raft; the kids and Grant found a maintenance tunnel and a golf cart that got them back to the visitor center, but in the film Zach and Grey scavenge a battery from a damaged golf cart and use it to repair one of the old Jeeps in the ancient visitor center garage so they can use it to get to the
new visitor center.
The old visitor center and most of the northern part of the island are the "restricted zone", off-limits to park goers, where much of the research goes on. The northern part of Isla Nublar, in the book, was the primary location for the original park, while the mostly-volcanic southern tip was more poorly developed and not well-surveilled. The raptor nest turns out to be in the southern part of the island. It was an interesting nugget to have the restricted zone be the northern part of Isla Nublar - and a bit of foreshadowing for die-hard fans as to the sorts of other things that would be up there.
In the book, the big rex gets into the sauropod paddock shortly after escaping and attacking the cars. (Muldoon pithily comments that she'll be having "fine dining tonight".)
I. rex's first target after wiping out the containment team is...the sauropod paddock, where she kills at least four animals before leaving to attack the kids and several
Ankylosaurus.
"Management" - Hammond - forbade Muldoon from having heavy weapons out of fear that the priceless animals would be slaughtered instead of retrieved; he eventually badgered them into giving him a rocket launcher, but it primarily fired tranquilizer rockets and only had six explosive shells (to deal with 8 raptors and 2 rexes, plus the dilos and whatnot). It wasn't the LAWs that he wanted, but it had to suffice. The park's primary containment gear was shock prods and nets, which were all too slow and useless.
Jurassic World has a similar setup: the ACU's shock prods and nets are slow and weak and can't do much to
I. rex, and only a helicopter-mounted minigun and a rocket launcher late in the film give it any pause. Owen tells management that the ACU's gear is laughably insufficient, but Masrani and Claire say that they don't want to turn the park into a "war zone" - parroting Hammond's line almost exactly.
Oh, and when Gray and Zach are riding the monorail into the resort from the port, you can see somebody behind them reading a book reflected in the glass. The book is, of course, Alan Grant's
Lost World of the Dinosaurs.
Gray and Zach also carry in a few plot lines from Tim and Lex's story in the novel. Their parents are getting a divorce, so they get to spend the week with Aunt Claire on VIP passes to see the park. That's basically the storyline Tim and Lex had going: their grandfather wanted to get their minds off their parents' divorce, so they would get to spend the weekend on his island resort.
Other aspects of the film owe their provenance to the franchise's fandom rather than to the books. The ultimate example is the climactic fight between the heroes and the
I. rex. To totally and utterly spoil everything, the raptors attack
I. rex but don't hurt it enough, so Claire goes and gets "more teeth":
T. rex, who she baits out of its paddock to fight
I. rex. Rexy and the raptors basically team up against
I. rex and win (with considerable help from a
Mosasaurus). The final shot of the film is of Rexy standing on one of the island's buildings roaring in triumph, once again master of its domain. Remember the outcry after
Jurassic Park III, when the
Spinosaurus aegyptiacus curbstomped a
T. rex and fans were livid? They weren't livid for the "right" reason;
Spinosaurus was a bigger, more powerful dinosaur, so having a
T. rex get rekt by it would make perfect sense. They were livid because the iconic Rexy got beat by some new punk dinosaur. Well, Trevorrow pitted the old fan-favorites, Rexy and the raptors, against some new punk dinosaur, but this time the old fan-favorites won.
Or the instance early in the film, when we first see a control room technician, Lowery, wearing a vintage original Jurassic Park shirt. Claire suggests that it's in bad taste because, y'know, people died. Lowery acknowledges this, but points out that the first park was totally legit. With his sarcastic asides on the unfolding disaster, Lowery stands in for the longtime fans. He also stays at his post until the end and survives, but he
does get friend-zoned by Vivian, who works next to him in the control room and who already has a boyfriend. That...that kinda sums it up right there, doesn't it?
And then there's the holographic
Dilophosaurus, in full movie frilled-dragon about-to-kill-Dennis-Nedry pose, that startles a raptor chasing the heroes through a building and allows them to escape.
Frankly, fans haven't got anything to complain about. In fact, the movie could arguably have been better if it
didn't bend over backwards to take
Jurassic lore into account; the final battle was awesome but goofy for the same reason that the fight at the end of last year's
Godzilla was kinda goofy: the "good" dinosaurs sort of teamed up with the humans to take down the "bad" dinosaurs. I mean...why didn't Rexy go after all the evacuees half a mile away after the mosasaur ate
I. rex? Why didn't it go after Owen, Claire, and the boys?