1. Well detailed bosses - Agreed. The three guys who show up in HR I never once cared for. They acted like stereotypical bad guys in every single way. The tank with the big gun, the silent assassin, and the weirdly accented leader.
2. - Lack of melee weapons - True. Wasting ammo on breaking crates is not cool, and ammo is scarce enough to start. While we're on this subject, however...
2.5 - Lack of food vendors - Did anyone else besides me find it agonizing how long you would play certain missions with only ONE energy cell powered in this damn game? Why didn't the food vendors in Hangsha, Detriot, or any other hub sell actual food since energy bars restore those cells? Yes, I know LIMB clinics did this, but in Deus Ex 1, you could also stumble upon plenty of ammo and restoration items with just some basic scouting.
3. - Lack of true specialization - I fully agree on this one. If XP/Praxis kits can let you unlock pretty much everything by playing a stealth character, which the game seems to force, there are some severe balancing issues to be sorted out.
Why not have skills be specific in how you progress, and Augments fill a general role in the same way? That's what the Skills/Augs let you do in Deus Ex 1. For example.
Swimming skills versus Augmented Lungs. One costs you skill points, while the other costs an Aug slot. So, which do you spend? The Aug slot or the Skill points?
That old system would've worked quite well in HR with enough planning. Augs are more powerful than skills anyway, so they should let you do more when you use them.
4. - Endings that mean something - There's that, but also don't forget that the endings of the prior two games had gameplay elements you could pursue to reach them.
Wantd to destroy the base with Page inside? Hack all the terminals correctly.
Want to go out guns blazing? Destroy his container and turrets.
And in IW, who would you side with at the base of the Statue of Liberty? They would all give you objectives to achieve to tip the scales in their favor.
5. - The lack of humor - This doesn't NEED saying. Deus Ex was funny at times, and it fit the mood perfectly, even with the diabolical things going on. In HR, it's far too bleak without much direct backing for it. We're told things about the world, but it happens offscreen or out of your reach most of the time.