Eidos Montreal was wholly aware that the boss fights were not consistent with the rest of game’s design or its vision. He noted that in the original design, boss fights “were meant to be like the rest of the game, where you have different choices – you can be stealthy, you can be lethal or non-lethal, you can be combat oriented.” Yet as so often happens, the team underestimated the time it would take to implement their design plan, and nuanced boss fights – along with extra city-hubs, weapons, and augmentations – were what got cut. Why exactly this decision was made so late in the design process, or why they weren’t able to complete it despite a four-year development cycle, remains to be seen.
Deus Ex: Human Revolution is an excellent game but it really was the forced linearity of the boss fights that kept it from being a Game of the Year contender. The first boss fight in particular is bad, because its an abrupt change in gameplay and as this Penny Arcade comic suggests you can enter as an unprepared "pacifist", clueless as to how to defeat the augmented super soldier. Here's hoping a sequel can advance the series' vision of universal choice.