Okay lets look at the whole Series, not just ME3 but the whole Trilogy. Humans are the newcomers, we basicly just went past our own Solar System and are in fact the new kids on the block. So far, so good. Now the whole inherent Plot of ME1 is to make Shepard into a Spectre, for political Reasons, but that gets sidetracked when another Spectre goes crazy because he found a God-Machine. So the Goal shifts, stop that guy before he screws everyone over. Thats the cliffnotes version of it.
Now in the course of that Game, you come more or less, face to face with said God-Machine, its so utterly Alien to every concept you have that it can only be described as basicly a form of Demigod in its own right. It thinks differently, it basicly at best sees you as a Insect to be crushed, if it even notices you at all when it steps on you. It has its grand Plan going and you arent going to stop it, you can try, but ultimately you will fail. You do fail, the only Reason that the Reapers do NOT win at the end of ME1 is because that Sovereign doesnt recognize you or any Species as a Threat at all and overextends itself to "squash that fly" as it were. You win, but only because the God-Machine made a stupid Move. Sure it cant take on everyone at once but it can still screw you over royally. The kicker? Sovereign isnt the only one. Its just the only one that was there right now, his Buddies are still around.
ME2 starts, Harbinger is the new big Bad now, since you managed to alert the Galaxy to their Presence, even though nobody really believes you, and destroyed one of them, they are taking it a bit personally, Harbinger basicly goes out of his Way to specifically kill you, they underestimated you one, but they arent going to do it again. Of course since getting to you will take a bit, they need someone else to do it. Collectors. They are shadowy and enigmatic enough for it to work, even if they arent thralls of the Reapers by default, they probably would work for them. So they get sent to kill you, its personal Vengeance, you killed a Reaper, so they now want you dead, you arent a Threat to them anyway, but they are seeing that they cant underestimate every Insect as well, so they may as well take care of enough Problems as fast as possible. Human Colonies get abducted, the Collectors are basicly beginning with the harvesting Process ahead of time, take out a bit of the Competition before the Reapers arrive in full force. Now they arent planning on killing you, if you pay attention in the Game, Harbinger doesnt talk about eradicating Humans, or any Species, they want to "ascend" you, to lift you up, to improve you, at least thats what it sounds like. They arent just going to wipe the Galaxy clean every 50.000 Years, nope, they simply harvest all the Species at their peak of Power, and create a new Reaper, a new Demigod. Essentially the Reapers up to this Point are all the previous Species of the Galaxy, one for each Species every 50.000 Year Cycle. Its a living History Book. They are preventing your Race, or any Race, from dying out. Maybe the first Reaper was a Species that lived extremely long, and they decided to upgrade everyone and themselves, to gain immortality, whether you liked it or not. Of course being that advanced, they also became to slowly see themselves as Gods, after all, you could barely scratch one, even as advanced as you could be. Their whole Plan is not to destroy you, they are preserving you, making your Species immortal for all Time. They arent thinking like a organic Species anymore, they are thinking essentially like Gods, they think they are doing you a favor and any Discussion to the contrary of that they simply ignore, because they cant be wrong.
Now ME3 comes along, the Reapers go after Humans first. Why? Sure they have a bone to pick with Shepard for being annoying, but not the entire human species. In fact, what makes us so special? Nothing. The only real thing that makes us creepy to the other Species is that we think outside the box, adapt to challenges and generally organize in what to them is a utterly alien Idea. But thats it, they have no Reason to go after us first, especially not in full Force. Their usually modus operandi is getting the Citadel and taking every Mass Relay offline, preventing any reinforcements or mode of travel. Why go for Earth first, ignoring all the other crucial Steps that would normally garantuee victory? There is no Reason. So of course it bites them in the ass after all, everything that was established as a perfectly valid Strategy, as the sure-fire Way to win, was completely thrown overboard for a Species that basicly just made it out of their own System and is less of a threat than say the Asari, or the Turians. But it doesnt end there. We have spent 3 Years finding a Way to stop them, stopping their Allies and even preventing them from even returning at least twice, or at the very least slow them down. But no, the Weapon to destroy them? The one Option to win the War, has been in our own Backyard for all this Time. We probably found it when we found the Outpost, or did nobody bother to check? Maybe it was in another Outpost on Mars? So we find ancient remains of a dead civilization on Mars and we are NOT going to literally put the Planet on its head trying to find more? We'd normally risk destroying the Planet to find every little Scrap of Tech or anything remotely similar that has value to us. But nope, nobody noticed, or nobody mentioned, except for the one Moment where it turns out that we need it to win. Deus Ex Machina. But the Problem doesnt end there, after all, it turns out the reason the Reapers exist is because that synthetic Life always rebels against their creators, yes its valid, we have seen that happen with the Geth. But you can make Peace with them, in fact they want peace, they dont hold Grudges against the Quarians. So the brilliant Idea to stop that from happening, is to come around every 50.000 Years and kill every organic Species, making them into a Synthetic Lifeform to do it to the Species in the next 50.000 Years.