Because the justification for the fanservice is absolute shit, and people get riled up over it. ('I breathe through my skin!' Then why do you wear skin-tight leggings?) Plus she can break the game a wee bit.
Yes and no. MGS5 is a great game, but it isn't a great Metal Gear game, if you get my point. If you want an interesting, if a little bit convoluted story, pick it up. If you're there for an answer to your questions... well, blame Konami. A whole story chapter was cut, and as such some of the endings seem a bit... forced. For instance, one ending just pops up out of nowhere on your mission list, with no fanfare or reasoning.