Dr. Wu May Have Toyed with Velociraptor Genes
Considering that Masrani Global (the new owners of Isla Nublar) toyed with dino DNA to create an entirely new (hybrid) creature, it stands to reason that the company's scientists could also have altered certain aspects of the velociraptor genome. After all, even in the early days of dinosaur cloning, InGen was making calculated alterations to their creations: denying embryos the possibility of a Y chromosome (to ensure all the animals were female) as well as engineering the dinosaurs with faulty genes that prevent production of the amino acid lysine (in case they ever got off the island).
According to that film, it was Dr. Wu that made the lysine contingency possible - and, since Wu is back for Jurassic World, it wouldn't be particularly surprising if the geneticist made adjustments to the park's most dangerous dinosaurs (once again). While it's not explicitly stated in the film, it's possible that Wu and Masrani engineered their new raptors to be slightly more docile and obedient - Wu even hints at this idea in his argument with Masrani, stating that none of the dinosaurs on the island are entirely authentic to their original species, and have been altered in subtle ways to make better park attractions. While the notion of nerfed velociraptors would be upsetting to series fans (and somewhat undercut the importance of Owen's relationship with the dinos), there's a precedent for the idea as far back as Michael Crichton's original story.
“The dinosaurs we have now are real,” Wu said, pointing to the screens around the room, “but in certain ways they are unsatisfactory. Unconvincing. I could make them better.”
“Better in what way?”
“For one thing, they move too fast,” Henry Wu said. “People aren’t accustomed to seeing large animals that are so quick. I’m afraid visitors will think the dinosaurs look speeded up, like film running too fast.”
“But, Henry, these are real dinosaurs. You said so yourself.”
“I know,” Wu said. “But we could easily breed slower, more domesticated dinosaurs.”
“Domesticated dinosaurs?” Hammond snorted. “Nobody wants domesticated dinosaurs, Henry. They want the real thing.”
“But that’s my point,” Wu said. “I don’t think they do. They want to see their expectation, which is quite different…. I’m just saying, why stop there? Why not push ahead to make exactly the kind of dinosaur that we’d like to see? One that is more acceptable to visitors, and one that is easier for us to handle? A slower, more docile version for our park?”
Hammond frowned. “But then the dinosaurs wouldn’t be real.”
“But they’re not real now,” Wu said.
Following the destruction of Jurassic Park, it makes complete sense that Masrani would be interested in taking added precautions - especially with the park's most dangerous inhabitants. What if Wu and Masrani executives both felt that raptors, in their natural form, were a liability and too hard to handle - leading to genetic modification that made the animals "more docile" and "acceptable to visitors"?
Obviously, Trevorrow doesn't turn the fan-favorite velociraptors into entirely docile shells of their former onscreen selves but it's not too much of a stretch, especially considering the series' ongoing thematic emphasis on humankind manipulating nature, that Dr. Wu could have done some minor tinkering with raptor genes/hormones in order to make them a bit more agreeable. After all, Jurassic World appears to be tightly controlled theme park - one that has learned from the mistakes of InGen's past, maybe that security came at a cost: significant genetic tampering.
The Enemy of My Enemy is My Friend
Ultimately, by the final act of the film, the situation is less black and white for the raptors - when they are torn between their former alpha (Owen) and a dangerous new contender for the title (one that shares raptor DNA). Ultimately, whether the raptors side with Owen to take on Indominus rex because of loyalty or self-preservation isn't entirely clear (it's probably a bit of both). However, there's no doubt that Jurassic World's velociraptors have determined Indominus rex is a greater immediate threat than their human captors - since the sizable hybrid is on a blood-soaked rampage (simply for the sake of sport and fun).
Taking into account raptor intellect, it's conceivable that the ruthless predators would want to eliminate any significant competitor that would threaten their safety (and future food sources) on the island. After all, this wouldn't be the first time that the raptors have attempted to takedown an apex predator - simply because it got in the way of their own feeding frenzy.
Still, the aforementioned scene of the raptors actively running alongside Owen's motorcycle in the jungle makes it clear the velociraptors aren't completely free-thinking strategists, and do, even by the end, respect Owen. It's conceivable that the brainy dinos are smart enough to understand they've got a good reason to assist Jurassic World's game warden - even if they are still far from being "tamed".
After all, the raptors of Jurassic Park III proved that the dinos aren't thoughtless killing machines and, depending on the circumstances, have spared humans they encounter - in the interest of more pressing matters (specifically the protection of their eggs).
Given the trust and care that Owen established with Jurassic World's velociraptors, it's not entirely out of left field for them to refrain from killing him, if he served to help protect their pack from annihilation at the hands of Indominus rex.
If you have your own theories, or can help fill in the holes in our own (or poke brand new ones), we invite you to share them in the comments!
Update: How it Should Have Ended has offered a fifth (tongue-in-cheek) theory of their own:
Jurassic World is now playing in theaters.