Just finished myself... (and it is one more of the "I dosed, tasered and beat people but killed no one"-category - I managed the "Pacifist"-achievement on "Give me Deus Ex"-difficulty)
I can only second what The E has said; Mankind Divided is clearly set-up as a 2nd of 3
the mid-credits scene basically ellaborates on the "full stop" the game does and sets-up a sequel; basically doing a "Next Time on Deus Ex: Adam Jensen Stories"...
Man, I totally forgot to write about why things mentioned in the spoiler don't work.
My main objection to the whole "Augmented as metaphors for victims of racism" thing is that most augmented people chose to be augmented (unless the DXHR universe is a place where industrial accidents are a common occurrence). Yes, there has been a horrific incident which explains the distrust for augs
To be fair, since Human Revolution they have been hammering -metaphorically- the point that people in their world got augmented because of job market pressures and if you go around in the side stories there are a lot of these quietly mixed in the world (remember the side stroy of DX:HR in Hengsha where you had to extort a Social Enhancer for the Tongs? The woman who had it justified getting the aug and loan which got her in with organized crime because she could otherwise not compete in her field as a glorified sales clerk)
... but yeah the leap is too big for the universe they have set-up
On another note, I noticed that I was quietly following the Aug-lines and Aug-train rules about three-four houres in -basically 2nd time you return to the Prague Hub- because I didn't want to get stopped again and again... Anyone else doing that? - Wonder if that just me being efficent in a game (esspecially since said game has severe frame rate drops and loading times on my rather-old hardware) or hinting a deeper weakness of my character...