The thing that bothered me about all the boss battles is that there was a cookie-cutter pattern, once you learn it it's just a matter of repeating the cycle. It's not challenging, it's frustrating. Replaying the boss battles doesn't come off as fun as much as it is tedious and monotonous.
Based on that brief interview with G.R.I.P.'s lead the was the boss battles have been designed makes sense. He clearly states he's a shooter fan, he states the cycle they used to create the boss battle formula (orient, observe, decide, act), and (as Sy mentioned) he openly claims that they don't have background knowledge on Deus Ex. I'm not sure the "arena" format even really works that well for a game that's not centered on 1on1 combat. It's kind of an odd choice to outsource such critical segments to a team that's so out of touch with everything else about Deus Ex conceptually.
Speaking of boss battles, I really don't get what was so hard about the second boss, Yelena Fedorova. I think I mentioned it earlier in the thread but I had no trouble with that fight at all, even on the hardest difficulty. Through my first two playthroughs I didn't even know you had to get her to "crash" into the electric generators; the thought never occurred to me since nothing about the layout really suggested it. In retrospect I should have paid attention to the wet floor. Anyway, I figured out my own little formula: stun her as she's dashing towards you, blast her until she recovers, rinse and repeat. If you're fast she can go down in two cycles without you even getting a scratch.