To make a very specific point, you have to understand that this entire thing is written from a very narrow perspective. There is no logical reason why organics and synthetics would need to fight each other. There are entire science fiction series that deal with what amounts to a positive relationship between organic and synthetic life, the most enduring probably being Asimov's writings ( the movie "I, Robot" is nothing like what he actually wrote or where it went by the end of the series ). There are problems with it as anyone who has read the books can tell you, but if I was going to create AIs for whatever reason I'd probably start by hard coding Asimov's "Laws Of Robotics" into them, heading off some of the problems from the series that would logically occur with sub-coding, and then just live side by side with them.
I find the assumption that people would just instantly try and kill AIs, or that synthetics would automatically decide to kill all the "inferious" organics to be inherantly flawed. I can see how that problem could occur as it's been spelled out in a lot of fiction, but I do not think The Reapers are correct in that it's inevitable.
I also do not nessicarly think that synthetics are inevitably going to win a battle against organics, especially in a world like Mass Effect where things like "Biotics" exist and are pretty much exclusive to organic lifeforms. That's something that can be argued either way, in general it being an uphill battle usually makes for a more exciting story which is why humans are always portrayed as being on the verge of losing. Interestingly a few universes like say "Space Above And Beyond" were written so that an AI war already took place and the AIs lost and were done with more or less. One of the themes there was that the remaining synthetics were siding with the aliens (Chigs) because of having lost the war with humanity.
In the case of ME3 I think the bottom line is that the ending is ambigious and it doesn't give any real answers, what is said is highly suspect at the very best, and we still do not know who created The Reapers, if they are still out there, and other assorted questions. The ending was specifically designed to inspire debate while ultimatly answering nothing of note in a definititve way. All we really now is that one paticular source has stated a possible motive for The Reapers and it may or may not be true.
Also as a side point, The Geth could have been squashed liked an insect at pretty much any time. They were an epic enemy for the creating race of Quarians who were left floating around in a space fleet they supported by scavenging, but not really for the Council or probably any of member races individually when you get down to it. The Geth were a fringe race and not really viewed as much of a threat until they started to invade with Sovreign and even after that they were largely being ignored because they weren't seen as being worth the time and expense for the major races to get rid of, because they had little of value that was worth fighting for and it would be an expensive proposition. As long as they stayed out in the arse end of the galxy nobody gave a crap. Heck, they arguably only have one planet (Quarian homeworld) by all accounts, to a race that has dozens or hundreds they probably seem lulzworthy.
Overall the whole attitude towards both the Geth and Quarians seems to be scorn. The major races are too busy with their own agenda to really care about helping the Quarians, which has lead to bad blood where the Quarians are treated like craptastic Gypsies, and the Quarians have become isolationists who in turn only care about their own issues. Just as the Council Races ignore human issues, they probably care even less about The Quarians who don't have the resources as humanity, a large fleet, but a scavenged one and they don't control any real colonies or resources for that fleet to present much of a threat. They seem to view pretty much all the other races the same basic way, even the ones like the Volus and Elcor that are allied with them. Heck I think the term "Client Race" has come up a few times, where it's pretty obvious that the minor races are basically paying off the major ones to toss them scraps and protection (The Turians are apparently paid to protect The Volus for example, and I believe there were even comments on how that effected the tax rates). A lot of which incidently contributes to why being "Renegade" isn't nessicarly evil, and is still doing pretty much the right thing for the right reasons. When you get down to it letting The Council die is something they kind of deserve because they are a group of buttheads who treat everyone like crap. The only reason why they have any respect for humanity is due to sheer power, Humanity has the abillity to fight, and produce and maintain large fleets, not to mention an infrastructure and resources.... unlike lesser species. Humanity might have lost in the long run but it proved itself a potential threat (and a definate power) during "The First Contact War" by having some success against the dominant military power. As the Volus ambassador spells out in ME1, it all comes down to your muscle... and The Quarians are in a bad place so even with a huge fleet they don't have anyone and get to be treated as dregs.... which is why "helping the quarians" has never justified a war with The Geth, there was nothing in it for the other races.
