I desperately wish for expansions, not just "tacked on DLC" like Mass Effect and similar have.
I would love an expansiony thing, similar to AssBro was to AssCreed 2, though maybe not with the same main character. There is a "time area" to explore here, akin to the star wars period between Episode 3 and "The First Real Star Wars", between the events of Sarif and Darrow, and the first Deus Ex.
Ideally: You would be able to choose which augmentations you get, either mechanical ones, or nanotech. There would be advantages between choosing which ones you get, or choosing none at all. Sort of like the humanity level in Vampire Bloodlines. Obviously, you would get stronger, and youd be able to pull off crazy shit, but youd risk "losing yourself", or not, as neither games (DX or DXHR) really go deeper into the subject of "are you still human, if augmented?" Of course, your appearance might change completely, or not at all, depending on if your augmentations are mechanical or nanotech (or whatever it was called in DX)
Also, I highly suggest making emails you read "register" in the story. Not just for quests, but for the main plot.
Also, if you are going to involve prerendered cutscenes: MAKE. THEM. LOOK. BETTER. THAN. THE. GAME, not worse.
NOTE: a whole slew of games came out, based on that star wars time period, and they were pretty good. Star Wars Empire At War as well as Force Unleashed (Atleast the first one) were all good games in their own right, and good SW ones. I think there is a lot of potential for a good DX game to be had there, especially since you might even get to meet the dentons or come up against fema, or have nothing to do with them at all, and have a brand new story, which only slightly is related to the main plotlines of the DXes.