What Was In-Gen's True Reason for Creating Indominus rex?
While Masrani commissioned the development of a bigger, scarier dinosaur to provide Jurassic World with a new attraction, the InGen board had larger (and more profitable) ambitions for hybrid-dino development. Foreshadowed by InGen's interest in weaponizing trained raptors, embodied via security head Vic Hoskins (Vincent D'Onofrio), Indominus rex was planned as a military asset. This isn't to say that Wu or Hoskins intended to use Jurassic World's Indominus rex specifically; however, at the very least the mutant creature was a test-run to help refine the manufacture of hybrid dinosaur soldiers.
For thousands of years, people have employed dogs and other animals in warfare - utilizing non-human evolutionary advantages (heightened smell, speed, and hearing, especially), to gain an upper-hand on the battlefield. Building on that foundation, Hoskins and In-Gen provided Owen (Chris Pratt) with funding to train Velociraptors - in the hope of replacing human soldiers with ruthless but loyal dinosaurs. Unfortunately, the plan wasn't quite as cut-and-dry as Hoskins hoped; yet, even though Jurassic World tumbled into chaos, InGen's goal of weaponized dinosaur hybrids was achieved.
In a brief scene that shows Dr. Wu escaping Jurassic World's genetics lab with frozen embryos, escorted by InGen soldiers, it becomes clear why the company would not allow Masrani nor Jurassic World's staff access to the complete Indominus rex genome: Wu's primary goal, working in collaboration with InGen's security arm, was to build a stealth killing machine under the guise of a zoological attraction.
Bribed by Hoskins, Wu tailored the Indominus rex's DNA (and subsequent traits) for durability and stealth - creating a monster that could be deployed at night (with thermal vision), strike quickly, and avoid detection from opposing forces (thanks to environmental blending and thermoregulation).
Given the number of well-trained Asset Containment team members and InGen security workers that lost their lives on Isla Nublar attempting to stop one Indominus rex, there's no doubt that, if dropped into a war-torn region, the hybrid (much less a pack of cloned hybrids) would offer unparalleled battlefield advantages.
After all, Masrani Global was not solely in the business of cloning dinosaurs, funding Jurassic World's reopening through telecommunication and oil industry profits, but the CEO's primary goal was akin to John Hammond's original dream for Jurassic Park: to create a place of wonder, where attendees, employees, and de-extinct animals can live in harmony. Considering Masrani's idealistic view, InGen's security arm concealed the plan to turn Jurassic World's dinosaurs into military assets from him - shoe-horning in dangerous evolutionary traits that posed a risk to the park, and would never have been included if Wu's primary goal was simply to make Indominus rex frightening to behold.
Ultimately, even though Owen was able to stop the rampaging Indominus rex (with the help of his raptor team, a Tyrannosaurus, and a Mosasaur), InGen and Wu still escaped Isla Nublar with decades of research and genetic samples - meaning that, while Jurassic World may never reopen, InGen's weaponized dinosaur program will likely resurface. After all, a Stegoceratops was initially planned to appear in Jurassic World.
It might sound crazy but given that Jurassic Park 4 was originally set to feature humanoid-dinosaur mutants, and since the franchise isn't likely to re-open Jurassic World, Universal Studios will likely want to keep upping the dino-rampage ante.
Time will tell what greedy InGen scientists cook up next but with Jurassic Park sequels already planned, and a major opening for Jurassic World in the books, it's safe to assume Indominus rex isn't the biggest or the most frightening dino-hybrid that audiences will see on the big screen.