I think it's a mistake for them to lay all the blame on the boss fights. The cutscenes in Deus Ex were also terrible. I personally opted to play the game stealthily and yet opening an arbitrary door would trigger a cutscenes showing Jensen blundering into a room like a moron. And there wasn't even any consistent with the checkpoints, as one boss fight it saved before you opened the door and the next would spawn you in front of the boss.
They should have opted for cutscenes using the in-game dialogue system, like Alpha Protocol. All the promotional material promoted the freedom of choice and yet the cutscenes and boss fights run completely contrary to that. You only have to look at a game like The Witcher 2 where you can choose
whether you want to fight the final boss or walk away. Same with Alpha Protocol.
I also found the game got a bit side-tracked towards the end. It started incredibly well, yet as you got further it was just one massive warehouse / open yard filled with soldiers after another. That's in comparison to the atmospheric, conspiracy based earlier part in Detroit and Shanghai. They just followed the typical FPS route where the further you get the more enemies you face, the stronger they are, the more weapons you need to fight them and you need massive robots or bosses and an increased difficulty to increase the tension. And anyone that wanted to learn more about the story would want to hack every computer and open ever storage cabinet, which completely through off the pacing.
Deus Ex: Human Revolution is a great game but I feel it would have been a lot better if they had really challenged the conventions of the genre instead of just incorporating them without any consideration. Cutscenes and boss fights are a dated concept, as is expecting 'hardcore' gamers to read every email, PDA, magazine, etc. And in terms of pacing I don't think any developer compares to Valve with the Half-Life series.
"The price of freedom is eternal vigilance."