I completed my first run of MD in 53 hours and it is the longest it took me to beat DX game (next is DX1 with 47 hours and HR with 40 hours) so I never felt like it was too short.

Other than that agree on visuals, Prague and whatnot. I don't think that characters were well written tbh except Jensen and Pritchard in his DLC. They were utter boredom who lacked meaningful screentime and huge stepdown from both DX1 cast and that of HR.

As for 'Mechanical Apartheid' thingy I think that as it is in game is misguided because Aug Incident of HR was much more nuanced than MD makes it to be, racism analogy doesn't work because natural people have really solid reasoning behind their stance towards augs which can't be said about racism irl and its portrayal is too black and white bordering on cartoonish. Discrimination and dehumanization would certainly follow but presentation as I said is cartoonish and the morals writers are deriving from it are to me one big headscratch in context of all that.