I don't mind them. Used right, they allow things to flow correctly, and retain character ability without sacrificing something like credulity. Uncharted 3's ending comes to mind. Since the villain was actually human this time around, and a shot to the head tends to kill any normal human, using an extended QTE sequence as the fight, across terrain, and interspersed with the normal melee/counter mashing of the rest of the game, it works quite well. When they don't break the immersion or are done consistently enough that it's a core mechanic, there's not really an issue. Guitar Hero and Rock Band were fun because of their song-based QTE's, after all.
As to the Prototype 2 final fight...well, that lackluster, abrupt fight wasn't exactly the highlight. Nothing as good, or as challenging, as the Prototype 1 fight, where you have multiple ways of dealing with the boss, you're on a timer, and there's all kinds of cluster fucking around you, getting in your way, messing with your controls, all that. That they peppered in the context-sensitive stuff with Mercer at the end made sense, given that there's a finite window where you have the upper hand, but still somehow undercuts how powerful Mercer has been up until now. Kind of sad, really.