I didn't see the earlier games' tone this way. ME1 ends up with a massed fleet pounding against a single Reaper, which isn't even fighting back but has already proven itself able to blow up our warships with ease. We do better in ME2, but we're fighting Reaper pawns rather than actual Reapers.
It's the genre convention. ME1 isn't a dark and gritty game that shows the real consequences of war and the reality of fighting an overwhelming foe. It's a B-movie plot about the ubermensch hero kicking ass and taking names. Like with any plot of that nature - see e.g. something like DA:O - the eldrich abomination is terrifying until it comes time to kill it, in which case you find the Macguffin of Villain-Slaying+1 and win out.
It's a bit like if Garraus, in one mission, just had his brains blown out all over a windshield with no warning and no follow up. That's realistic - that's how people die in war. But it's also ridiculous and inconsisent with the genre convention.
This actually makes a bit more sense when you realize that those are two different "you"s there-- the first is the organics of this cycle, the second is organic sentients in general; it's the semantic equivalent of saying that you cull deer to keep deer from starving to death. Not great, no, but after the hole Bio dug for themselves with the Reaper motives, it's hard to come up with something better. This board's never managed it.
The problem isn't coming up with a motive for the reapers. It's coming up with a motive for the reapers that isn't pure, absolute and ireedemable evil. When your plot is Space Nazis who repeat their Final Solution to the Organic problem every 50,000 years, you're not writing about a morally complex problem with no easy solution and no obvious villains. When you ask the question "When is genocide, perpetrated by the means and technology more awful than what the Nazis used, OK?" you're not going to get a sane answer.
As to your point, well, not exactly. "Organic" life, as I like to say, includes the intestinal fauna responsible for farts. But no one cares about saving the fart bacteria. What people really care about in these types of things is sapient life, and then you run into the problem of having to draw up a reason as to why this kind of sapient life is somehow more intrisically deserving of life than this other kind of sapient life, which ME3 doesn't do. ME3 wants to say that being made out of meat is special, without ever providing a reason as to why meat is special.
The analogy to culling deer is just semantic; it's not an analytical parallel. (Edit: On second thought, it's not a semantic parallel either. Because the threat is hypothetical in the case of the reapers; it's "we'll exterminate organic life so that possible future synthetics don't end up exterminating organic life", but in the culling situation, inaction will lead to guaranteed extinction).
First, the reapers actually leave the continued existence of "deer" up to complete random chance: the next crop of "deer" could just wipe themselves out before ever becoming spacefaring. And it may be that no more new "deer" will spontaneously evolve - the reapers might just run out of them. The only way the logic works is if - until the end of the universe - there'll be an unlimited stream of incoming organic life. Essentially, organic life has to be self-generating.
Second - and this ties in with the first problem - if organic life is self-generating, then there's how would it be "wiped out" even if an AI species killed of all the sapient organics it found? More organic life would just sprout somewhere else. The AI would have to be self-sustaining for eternity, and it would have to effectively go around exterminating all other forms of organic life until the end of time. But that wouldn't "exterminate" organic life - it would just be the reaper cycle, but with more interruption and (ironically) genocides on a smaller scale.
Third, "AI" doesn't have to be made out of so-called "synthetic" material (which really is just material that's designed rather than material that sprounted into existence by random chance). You could just have an "organic" race genetically engineer a new form of life. It would be "artificial" intelligence that happened to be made out of meat instead of metal. On the necessary assumption that it has to (1) be self-sustaining for all eternity and (2) wipe out any and all other form of organic life, what you end up with is an enternally existing form of organic life that will never die out.
For reaper logic to work, the problem can't exist.
But this was a thing in ME1. The writers don't seem to have appreciated how thoroughly ME2 trashed the idea. Or ME3, which I think is why Gaider said that the best Rannoch resolution was a mistake.
Not really. The idea is incomprehensible nonsense because, as I said above, it starts from the assumption that being made out of meat is special. Even if peace between the Geth and Quarians wouldn't have been possible, the point wouldn't be any less stupid.