Let me say that I did enjoy playing Dishonored for the time that I played it. I went through attempting a no-kill no-detection playthrough on Hard. A few mistakes on my part here and there prevented me from the unblemished record, but hey, c'est la vie. To my topic however, there are very few similarities to Deus Ex, assuming we're talking about The Conspiracy and not the two followups (Invisible War and Human Revolution) that failed in comparison.
1) Story: Let me repeat. Story. Dishonored features a predictable series of events featuring a faceless (except for wanted posters I guess) and voiceless protagonist. The cast of characters is unimagined, and the best of them (Sam and Emily) still come off as tagalongs intended to move the plot rather than add anything to it. I also found that the game did a poor job of making me care about my targets. The books were a nice touch to get you to understand the lore, but they didn't really contain anything that couldn't have been implemented as part of the story. It's the old style of "show not tell" that seems to be going away in this generation of video games.
On the flipside, there have been few games since DX: The Conspiracy that present such intricate characters who actually seem to battle with morality. Sure they were also archetypical, but they felt genuine instead of being plot devices. It tackles issues with global consequences, and makes them feel actually pressing at the time. Your journey spans the globe, implying the gravitas of the situation while also making you seem small in the grand scheme. A dystopian near future that seems like an all too real possibility. Also, JC Denton is a man who has a face, can speak, and make real choices. He doesn't just blindly follow.
2) Skill Progression. This was my biggest disappointment in Dishonored, to be frank. I have "The Outsider" come to me in a dream and tell me that I now can use his powers because I'm an interesting person. When I wake, I have access to everything right off the bat, all I need to do is gather Runes and unlock them. While I thought the lore was interesting, I was immediately taken out of the character when I found I could just do whatever because some "Outsider" told me I could. On top of that, there's no real reward for playing THROUGH the game as everything is presented to you from the start. Sure, I need to gather objects, but once I have them, then what? I've got the powers I need (which if you're playing no-kill no-detection, is basically two powers and the agility passive), so I have no need to collect these runes anymore (I seriously stopped playing for a couple days because nothing URGED me to get back in and play, other than the need to finish). Bone charms are actually neat, but help in the smallest of ways only, still a nice addition. Where's the customization? It's a game produced by Bethesda, how about some choice?
Let's compare this to Deus Ex, since it's the IT thing to do. You are a cloned version of your brother who has nano-tech augmentations that elevate you to another level. Through the course of the game you come across augmentation canisters which allow you to choose one of two available augments for that canister (i.e. Lifting Strength OR Melee Power, not both). You then need to find Generic Upgrades for you to decide where to put them. What is interesting to note is that you have to progress through the game to find these canisters, you're not just given them from the onset. There's a tangible need to continue to play, as you will progressively become more impressive and capable of doing more things as you play longer. On top of this, the Augmentations are actually a part of the character, rather than being "God given", and in obtaining new ones, you feel as though Denton actually changes. These augmentations DRASTICALLY change the way you play through the game, and there's the fact that you miss out on getting the other powers; choose wisely. This functions two-fold: It makes the playthrough feel organic and tailored, while also necessitating the want to play through it again. Dishonored allows you everything, so go ahead and play around, there's no need to worry about missing out on a power.
Oh, there's also experience towards certain playstyles in DX, (i.e. Rifles, Multi-Tool, Medicine, Environmental, etc.), so it actually allows for more customization. There's a finite amount of these points, so again, choose wisely.
Overall, I find that the only comparison one can make between Dishonored and Deus Ex: The Conspiracy is that they are "open-path stealth games". Deus Ex was a genre-defining game that featured an intelligent story with interesting characters, while presenting you with a myriad of choices and styles of play. It really benefitted you to play through it twice if not three times to see all there is to see. Dishonored, while fun and interesting, feels shallow and undeserved of its great praise. An unimagined and hackneyed story with an uninteresting main character (seriously, what was stopping Corvo from being a thinking person instead of a blind follower? "I will say nothing when accused of murder! I won't ask about what other routes I can take, instead Sam will tell me on the boat in to shore! Hooray for being led!"), while also featuring shallow skills. Dishonored gets points for design, choices in routes, the chaos system, and fun. It is short, and undeserving of another playthrough though; I don't need to play as a ruthless murderer to guess the different outcome, when the process of getting there feels no different. Through all of this, it was still FUN. So by no means did I dislike Dishonored, in fact it's quite the opposite. I would put Dishonored in my handful of games that impressed me this year, for sure.
So please, can we stop comparing Dishonored to Deus Ex? They are both good, and both fun, but not terribly similar beyond the ability to "find new routes". Dishonored is Dishonored, not Deus Ex, and not Thief.