^^ It's not the same thing at all 'if you thought about it' and most importantly your missing the point entirely about Context.
With a first person shooter - it's exactly that a shooter. Moreover a war shooter then you are in acceptance of the mechanic of shooting wave after wave of enemy.
Besides as I have already stated - I do grow bored with their repetition although I accept it.
With Uncharted there is a different mechanic and context to the whole thing - it's an 'adventure' game in third person. It is not solely a 'shooting game' and therefore when presented after a thrilling set piece or exploration section with an open space with characters ABC jumping in to attack - survive that wave - only for same pirates ABC to jump in yet again. Repeat a few times and then game lets you progress.
Also with a FPS including COD you do not have to shoot 'EVERY' single person, but merely survive and move from A-B. With those sections in Uncharted you had to kill all those enemies before the game let you progress. There was no other choice. No way of bypassing the mechanic, by sneaking around and avoiding the confrontation.
In a game where adventure was the key word - the lack of choice and option in those sections sucked ass and whilst killing wave 1 of enemies would have been enough, when it asks you to kill 3 or 4 waves just because it thinks it extends the gameplay and makes the game tougher then the joke begins to wear thin.
All about context and the way the game presents itself. Uncharted sections like that sucked.