After discovering that more dinosaurs might have had feathers than previously thought, the JP3 design crew thought that adding quills to the backs of the heads of the males would help adhere to that, but not cause the audience to think that Velociraptor was not included in the movie, because what's JP without Velociraptor?
Also, about the higher organization of the pack, that's because it was around that time that dinosaurs were WAY smarter than people usually thought, including dromaeosaurs.
But in the JP fan universe, it's widely believed that the JP and JP2 raptors are classified as Velociraptor antirropus nublarensis (since they were supposed to be put on display on Nublar) and the JP3 raptors were V. antirropus sornaensis, since they were only found on Sorna and Hammond's people wanted to keep them there.