To be fair, the original DX had its fair share of cackling old dudes in towers. The villains are primarily rich CEOs or government leadership.
To elaborate a little, Deus Ex and Invisible War are fundamentally about the intersection of technology and human nature. You've got the Bob Pages and the Morgan Everetts. You've got the World Trade Organization and The Order, which are just two branches of the same entity. But they're not the source of evil where removing them fixes anything. I think where a lot of cyberpunk goes awry is that it wallows in the dystopia. Its characters are rebels. They are defined entirely by their opposition to the tyrannical status quo. They don't have much going on outside that. These narratives tend to go in one of two directions. One, humanity is doomed and dying and let's just ride it out. The likes of Blade Runner, and games like Observer -- they don't have any actual solutions. The world is rotting, run by corporations that are gonna bleed every putrid drop of blood for short term gains. Two, bring an end to the tyranny. Smash the state. Something like Tron falls into this category. It's not traditional cyberpunk, but it's a good example. Malice for the sake of malice. Remove the malicious element, and people will live in peace and prosperity. This is the dream of most revolutionaries. But it often doesn't end the way they thought it would.
Where DE/Invisible War differerent to a lot of peers, I feel, is that they examine the alternatives to a highly technological society dominated by corporations sometimes run by "nice" people, sometimes run by outright dicks. And the central theme is the problem of human nature. I always felt Helios was the philosophical linchpin of Deus Ex. Technology could allow us to have a society where everyone is fed. Everyone is clothed. Where the lights are always on. Where everyone's voice is heard at a political level. But. This kind of utopia stinks of tyranny bent into a different shape. When you ask people to solve the problems that face humanity, their solutions are often varying degrees of fascist. They just don't realise it. They don't quite think it through. And to some extent this is a religious parallel. To create a society free of injustice would require this entity -- an AI or a literal god -- to peer into the minds of every citizen. To know what they truly want. What they truly believe. At this point you've basically got a theocracy of some stripe.
In the original Deus Ex, Helios lays out its plan, and it has merits.
But in Invisible War, the plan has some glaring issues that Helios handwaves with, "Upon consideration, you'll see that this arrangement is for the best. 'General ideas are no proof of the strength, but rather of the insufficiency of the human intellect.' The words of Alexis de Tocqueville, an observer of the birth of modern democracy. Though general ideas allow human minds to make judgments quickly, they are necessarily incomplete."
I always liked that because I feel cyberpunk narratives flip-flop between "OMG the acid rain is so aesthetically sweeeeeeeet!" and "If we got rid of the evil corporation, it'd be sunshine and rainbows." But Deus Ex meditates upon the various solutions to tech-driven tyranny and how each solution gives birth to further tyranny. Helios asks the question, "Is it freedom when one child is born to poverty, a chance combination of organic materials, while the wealthy child is shaped every day of his life, enhanced genetically, trained, educated, often augmented nanotechnologically?" That is a damn good question. But the only practical solution to such a problem can -- and probably will -- go horribly haywire in various ways. We have to do something, but all the somethings suck.
We know the world is unjust. But we cannot agree on how to make it more just without creating further injustice, at least that seems to be a recurring theme in government that translates well to a cyberpunk setting. The reason cyberpunk stories often gravitate towards AI governance is that even though they more often than not go down the "CRAZY AI DOING EVIL THINGS BECAUSE CAPITALISM IS EVIL AND THE AI WAS CREATED BY CORPORATE INDUSTRIAL INTERESTS OR THE AI IS BATSHIT CRAZY OR THE AI IS LITERALLY JUST GERBIL HOOKED UP TO A COMPUTER" route, there is a recognition that even in a perfectly balanced society geared towards goodwill and harmony, human nature will screw it up. At their heart, humans don't want to be free. But they think they want to be free. What is "freedom?"
We will always find ways to create underclasses. People shunned by your utopia because they didn't like some aspect of it. When Helios is asked, "What if I don't want you peering into my mind?" It flat-out refuses to give an actual answer to that question, pulling the "if you stop to think I'm totally in the right here". One could draw a parallel to many real-world issues. For example, smoking. You have a system in many countries pushing people to stop smoking. Taxing cigarettes heavily. Barring smoking from public spaces. Even get to the point of not being allowed to smoke inside a building you ostensible own. It's all very "for your own good, making a better world", and stuff.
But what if someone WANTS to smoke. They know it's dangerous. But they want to. Many lines of intersecting rights can be cut. But what underpins such a situation is this new breed of dystopia that I think has come more common in western societies. Societies that on the surface seem to be all about the rights of the individual, of fairness and equality. But there are weird things under the surface. They don't march into your house and take stuff away from you. (Not to downplay examples where that does happen.) No, it's more insidious than that. They start from the premise that any sensible person supports their position that "we must end XYZ", and then they start attempt to eliminate what the see as improper behaviors or undesirable elements. At some point we cross this weird line. We go from "Hey, I can ride the train or plane without breathing in smoke. That's okay" to "Nobody should be allowed to inhale or exhale smoke anywhere. We're not saying you can't smoke. We're saying you can't smoke in any of these locations that are just coincidentally everywhere under the sun."
(It's been kinda weird to see a lot of people being on the "purge smoking from society" bandwagon but also be supportive of legalized cannabis. It's almost doublethink to some extent. I think a lot of people don't even realise their position is contradictory. Banning smoking is a liberal political position. Legalizing weed is also a liberation political position.)
And then before you know it, there's no smoking in Disney films. People who were smokers in real life can no longer be depicted as smoking. And that superficially seems okay. It's Disney. They've always been wacky. But then Disney starts buying huge chunks of the entertainment industry. Suddenly there's no smoking in any new movies by any companies controlled by Disney, and that is a shitload of movies. Which is actually a remarkable example of how the entertainment industry being owned by a tiny number of companies has odd side effects. The James Gunn thing is another example. Disney fired him. Okay... Well, he's also fired from everyone that Disney owns. Which does come back to the unique nature of corporations in their ability to be kinda tyrannical.
I'm sure some people see that as no problem. They think smoking is a rotten habit that should be consigned to the dustbin of history. But there are implications there. Concerning implications for how we've created this new type of smarmy tyrannical corporation that is super inclusive and friendly and loves the whales and loves the baby seals, but underneath it is ruthless towards groups it has a beef with and is kind of a dick.
Cyberpunk narratives always assume the evil corporations are doing evil science experiments in their basement. (Deus Ex included.) But evil corporations in the real world? Not so much. The love of money may be the root of all evil, but many bad people do bad things for very noble reasons. It seemed like a good idea at the time. The benefits outweighed the risks, that kinda thing.