First, I'll be spoiling Deus Ex: HR, so stop reading if that's a problem for you. Second, if you please, watch this live action ad that was used to market Deus Ex: HR.
It's meant to be a propaganda piece of the anti-augmentation group in the game, Purity First, but the criticisms and issues raised are the kind of things that ideally would be primary components of the game's themes and focus. Granted, one of those issues, neuropozyne addiction, is a plot device that isn't necessarily intrinsic to the issue; human augmentations in the game have an issue where the body rejects them, and neuropozyne is not so much an "addiction" as it is an anti-rejection drug that is arbitrarily expensive. It turns out the companies don't do this on purpose to indefinitely milk people for money; they actually can't find a way to make the body accept the augmentations, and it's a really big deal when they discover that your character, Adam Jensen, has a mutation that allows him to accept the augmentations permanently. So that issue is given a lot of visual focus in the ad, showing people out on the street without the drug, but that turns out to just be a temporary setback of medical science.
That aside, the other issues all stand. What it means to give up your humanity, everyone getting into this arms race of augmentations to be better than the competition, how it changes warfare, how the augmentations make you dependent on corporations for maintenance and repair, and that they could track your personal data in a similar way to smartphones; all interesting social and ethical issues.
That live action trailer/ARG site for the game actually handles the moral and ethical quandaries of human augmentation in a much more interesting way than the game ever does. It's like an ad agency came up with this super interesting ad campaign, then the devs went "Oh wait, shit, the game is 90% done and it's too late to make the plot about exploring these issues AT ALL. Oh well." Should we call that Dead Island Syndrome?
My Summary of the Plot, Which Will Be Hard to Follow If You Haven't Played The Game
The whole game you're basically just obsessed with finding the mercs that killed (actually kidnapped) your old flame Megan, and you also spend goddamn forever tracking down this mysterious hacker from the Sarif factory early on. Then after you find him and sneak into Tai Yong Medical and accomplish nothing, you go to Montreal to find out that Picus invents/controls the news (appropriate for cyberpunk dystopia, but irrelevant to Adam's personal motivations and the augmentation themes in the game). You get to Megan who actually doesn't give a shit about being rescued, and Adam's relationship with her is this completely unresolved plot thread, despite seeming incredibly important in the first 15 minutes of the game. Then you spend the last 5% of the game worrying about this chip that is fucking up everybody with augmentations, then suddenly the game gives you the ending choices that are more about "Are the people prepared to know the truth about how much fucked up shit went down and who was responsible?" and really not at all about the ethical issues of human augmentation. Instead of addressing actual issues with augmentation I mentioned earlier, you have to blow up this absurd device that allows the Illuminati to mind control anyone with an augmentation.
Your ending choice just affects which political group is to blame for the big fuck up, and that affects public opinion on augmentation and how much it is used in the future. Sadly, like modern politics, it feels like your choice is based less on underlying ideals than it is on "Most of these leaders are dicks, I will vote for the one leader who is less of a dick."
Admittedly, it's easy to make a cool 3-minute short film thing with sick music in the background, and it's much harder to write a lengthy narrative that adequately uses those themes, but Deus Ex: HR didn't really even try.
The main characters in the game just don't have much complexity. Everybody who is pro-augmentation is a slimy businessman or Illuminati, and everybody who is anti-augmentation is basically a "sanctity of the human body" zealot/terrorist who is as closed-minded as anti-abortion advocates. A lot of time later on is spent uncovering the ways that these men have lied to Adam/the public (causing you to question their integrity), but less time is given to their personal beliefs about augmentation. Megan is a soulless scientist who is fine with doing horrific research because it's scientifically fascinating (what a delightful trope to continue to pass onto another generation of youth), and Adam has all of the philosophical depth of a beat cop; it's very hard to find dialogue choices where he gives any opinion other than direct, practical assessments of what is happening, and his thoughts on augmentation are "I was made half robot against my will, oh well, guess I gotta live with it. Pretty sweet that I don't have neuropozyne dependency for some reason, I guess."
There are a bunch of text logs and books and emails you can read, but the emails realistically capture how mundane 99% of emails are, while the books mostly just give factual accounts of the game's fictional history and fictional medical advances in human augmentation. There are a few Purity First pamphlets, but they read like the writing of religious zealots and don't explore the issues.
The one place they almost succeed is in conversations between NPCs in the city areas, who seem to always be having fairly candid conversations about the world they live in, sometimes discussing thoughts on augmentation. Unfortunately, some of the conversations are played for laughs because the participants are uneducated or ignorant, and even when they're not, they're almost always laypeople who only have a basic opinion on the topic. The bigger issue is that these NPC conversations are at best like 30 seconds long, which doesn't let them explore the topic much, and that many players don't have the patience to sit around listening to NPCs prattle on for 30 seconds.
Square Enix (or Eidos or whatever) will definitely continue the Deus Ex series, but it's unfortunate that they didn't do more with this story set at the dawn of human augmentation. The vast majority of your time is spent chasing after various elusive objectives, and the conclusion of those major objectives usually just meant a simple reveal of who was responsible for an event, or where to go next to get more answers. The protagonists of past Deus Ex games have never been particularly verbose, but they would occasionally let slip some interesting opinions; Adam almost never does this in his quest for answers/Megan. I would've vastly preferred if he was more of a...Solid Snake, I guess, if that meant he would occasionally engage his allies, adversaries, and superiors in some kind of discourse related to the themes of the game.
I feel like there have been big budget games that have bothered to explore the issues inherent to their fictional universe, even if they get a little pretentious or preachy about it. Metal Gear Solid and BioShock come to mind; I haven't played them, but perhaps Binary Domain and Spec Ops: The Line also explore interesting issues. But Deus Ex: HR is not one of those games. A film like District 9 can have a fantastical premise still used effectively to make the viewer think about issues of technologies that change society and how corporations will want to use them, and can have relatable characters that still make for an engaging story. Sadly, few games achieve this feat. The ending cinematics of Deus Ex: HR pretend that the whole game was leading you towards this philosophical choice, but the reality was you were tasked with chasing after uninteresting villains, and the game gives the player barely any context about the implications of human augmentation.