I've come to realize that the reasons people say that the Mass Effect 3 explanation of Reapers and their motives don't make sense simply stems from them absolutely not understanding it at all in the first place (I know, what's new... entitled gamers at their finest).
Among the arguments I've seen, three are most prominent. 1) The Intelligence says he wants to preserve organic life but uses the Reapers to just kill a bunch of it, 2) the Intelligence claims the Reapers are necessary because of the inevitability of conflict between organics and synthetics despite Shepard's actions leading to peace between Quarian and Geth, and EDI's relationship with Joker proving otherwise - assuming the player choices lead to those results, and 3) the Intelligence supposed "false analogy" with fire.
As for number 1.
I guess these guys just missed the hundreds of times it's said in the game(s) that the Reapers HARVEST advanced civilizations. The Intelligence at the end of ME3 says it outright: organic life is STORED in the form of the Reapers so that it's not lost forever in the conflict between machines and organics, a conflict that has always happened without fail, resulting in entire civilizations getting erased from existence. The ones harvested by the Reapers are integrated in them and assume that form, which is preferable to otherwise inevitable deletion.
As for number 2.
That's just cherry picking and doesn't "prove" anything, let alone that the Intelligence is wrong about the inevitability of war between synthetics and organics. Sure you can make it so the Quarian and the Geth reach peace, but that doesn't change the fact that two wars still happened between them before that, leading to the Quarian race seriously risking extinction, and also similar wars had happened in the countless cycles before Shepard's, without fail. One exception in one cycle doesn't mean anything. Just because peace is possible doesn't mean it WILL happen and certainly doesn't change the fact that conflict still DID arise.
And number 3.
It's just not a false equivalence. The argument supporting that it is basically says that fire has no free will when it burns, whereas the Reapers do. So the Intelligence claiming the Reapers are like fire, simply doing what they're meant to do rather than actively being interested in was is bullshit.
Except it's all wrong.
The Reapers DON'T have free will. Being sentient and acting high and mighty when you talk to them doesn't mean having free will. Once again, the Intelligence spells it out for your dumb asses at the end of the game: they're his tools. They're his means to achieve his goal, they do what he wants them to do. "My creators gave them form. I gave them purpose." Just another line a lot of pointlessly angry people missed, apparently. The Reapers have no choice in what they do. Whoever controls them (including Shepard himself in case you choose the Control ending) gets to decide what their purpose is, and they simply act upon that purpose with no decision making of their own. Just like fire burning a wooden log isn't "at war" with that log, the Reapers aren't "at war" with organics. They just carry on their function, nothing more.
Even when you talk to them, they are so detached, deadpan, they keep saying "there is no war, only the harvest". Cause they don't give a **** about war, they're not "hostile" per se. They simply do what they're made to do, period. Of course you as a player are guided (intentionally so) to perceive them as the enemy throughout the games, to think that they actually have ill will against the Galaxy. But it is explained pretty clearly by the end, they have no will in the first place, besides that of whoever controls them.
Frankly, it's beyond me how so many people just missed all of this. Although to be fair, they more likely just intentionally ignored it to justify their personal dislike towards the ending, but it's not like that makes it any less irritating.