I just think it's funny when people complain about how you don't have a "choice" when it comes to fighting the bosses, as if that somehow undermines the rest of the narrative of the game or something. The entire point of the boss battles is that Jensen doesn't have a choice because he is trapped with his back to the wall. There is literally no other option for him but to fight and hope to survive, so why does that hurt the overall narrative structure of the game? When he has the option to be either stealthy or go in guns blazing you can make that choice, but sometimes you don't get the luxury because the situation catches you off guard and forces you to work with what you've got.
As far as what the boss battles add or take away from the game in terms of the gameplay that is an entirely separate discussion. Personally I'm with you, I like the change of pace and full on combat focus of the boss battles, it helps keep things interesting. Either way they are short and infrequent enough that I would only see them as a minor issue even if I didn't enjoy them.