When comparing the similarities between two shows, some may not think to compare The Boys to Mr. Robot. They seem as different as night and day, but given a second look, the two are very much alike. Even though one is based on a comic book and has characters with literal superpowers, both work at deconstructing the illusions of reality by being brutally honest about capitalism.
Strip down the shows to the bare bones, and they share the same plot, featuring a "nobody" who tries to uncover the truth regarding a huge corporation after suffering a personal tragedy at the hands of a villain working for something worse than expected. The "worse" here are Vought International and E-Corp; however, one of them is truly the worst.
The Boys is about a group of vigilantes working to take out superheroes who pose a threat to society. In the series, it's revealed that "Supes" aren't born with their powers, but they are given to them by a substance called Compound V, which is created by Vought, a domineering corporation. It is responsible for creating The Seven, a specialized group of superheroes. Several Supes do Vought's dirty work, while the company looks to make a profit anyway it can.
In contrast, Mr. Robot is much more grounded in reality. The series follows a troubled young man, Elliot, who is obsessed with taking down E-Corp, one of the world's largest corporations. The series can be viewed as a companion to David Fincher's Fight Club, which served as an allegory on mass consumerism. E-Corp is a company that works hard at becoming the sole moneymaker of the modern world, and it manipulates the market while also buying out all competition.
At first glance, it's easy to name Vought as the more evil of the two. E-Corp is not much different from real world companies, and it's not experimenting on babies and innocent people, like Vought is. While E-Corp seems like just another corporation, it is actually more frightening.
Frederick Vought, the founder of Vought International, started his work during World War II when the Nazis were conducting human experiments, and Vought planned to make a "Master Race" composed of people who were immortal and invulnerable. The groundwork of Vought is rooted in racism and hate, as well as a desire to incorporate the Supes in as many positions of power as possible, like the military. However, in Season 2, it's revealed Vought is primarily a pharmaceutical company that wants to become the owner of the world's most desirable product.
This opens up a few problems that would eventually turn the company redundant. Even though Stormfront claims Vought had a plan for "everything," there doesn't seem to be an answer at this time for what happens if Compound V adapts to natural reproduction, especially since it appears to dramatically slow down aging in some cases. This would eventually lead to the demand dying down if its properties were being genetically inherited, like with Homelander's son Ryan.
While it seems Vought does not want this to be the case, the company has struggled to keep a lid on Compound V since Season 2 started, thanks to human factors like Homelander and Starlight. On top of this, Vought is clearly a heavily fictionalized version of big corporations. No matter how accurate the depiction of supply and demand is, it's easy to look at Vought and know it came from a comic.
E-Corp, on the other hand, has the capability of being a real business. There's nothing outwardly sinister about it other than being just another company. Furthermore, it doesn't have a real agenda beyond profit, unlike Vought, which is playing the superhero game, despite pharmaceuticals being its focus.
One of the major plot points of Mr. Robot is the chemical leak that killed roughly 26 employees, including Elliot's father. E-Corp covered it up, and after an fsociety hack, it's revealed the company knew all along about the malfunctioning system, but it decided against fixing it to save money. The company got away with murder without even a scratch to show for it. Its blatant disregard for its employees, as well as its willingness to cut corners for profit, are despicable.
Just like how The Seven are the mask of Vought, E-Corp is the mask of the true villain of Mr. Robot, The Deus Group run by Whiterose. The Deus Group hides in the shadows, manipulating world events for its gain and practically running the planet. This is thanks to the fact that it uses two of the world's most important resources against the population, getting excessively rich off oil and collecting personal data from the Internet.
This is the real difference between the two companies. Vought puts a target on its back by flaunting the Supes as a distraction from its true work; however, this poses a risk if the Supes get out of line. E-Corp, on the other hand, primarily keeps its dealings in the dark. Vought looks like child's play when pressed against the mastermind of E-Corp; therefore, it's the true winner of the evils. If put in the same world, Vought would control its magic pharmaceutical product while E-Corp controls Vought.