It's something not enough people understand or appreciate: the more freedom allowed, the less of a storyline focus we can have.
And because Deus Ex: Human Revolution features an in-depth plot within a freedom-based structure, many have complained about the scripted events; i.e., the boss fights. But in speaking to Edge , Eidos lead designer Frank Lapikas explains the necessity of boss encounters for the sake of the narrative. After saying it was a "narrative decision," he added:
"The whole game is story-driven so if we gave all these opportunities to get through the bosses it created some headaches for us to get the narrative to work, so we had to make that decision."
We can only imagine the headaches generated by making the game as free and customizable as it already is. Remember, it's not the existence of bosses that irritate some players, but the fact that you really can't fight them any way you wish. That would fall in line with the spirit of the game, of course, but as Lapikas says, it wouldn't fit the storyline. Personally, I found it a little irksome that I couldn't deal with the bosses stealthily, but whatever. It offered a nice change of pace for me.
The only thing that bugged me was that I had to keep at least one piece of heavy weaponry in my inventory all the time, just in case. That worked out, though, and besides, it's not necessary as the game does give you the weaponry you need during or just before boss encounters.
Related Game(s): Deus Ex: Human Revolution