It's all totally speculation. I have no way of knowing what the writers of ME where thinking about. I can only tell what my interpretation of what is stated and what is inferred in the game.
To me it's inferred that the intelligence created by Leviathans race, has deduced that all life forms/races/species/civilizations eventually follow the same sociopolitical patterns, regardless of their physical construction or properties.
And apparently (or according to the ME writers) it's an inevitable conclusion, that life forms will create "thralls" either through conquest or construction (enslaving "lesser" races or building computers/robots) and that these "thralls" will eventually equal and/or surpass their masters and destroy either their makers, themselves or perhaps even both.
At least that's the way i interpret what Leviathan, the Catalyst, Sovereign, Harbinger, Javik, the Prothean A.I. plus other sources are saying.
So Reapers could quite easily be less advanced by organic standards in some ways than say EDI or the Upgraded Geth, because they haven't changed or altered there original core functions.
What has been changed and how that's done to EDI and the Upgraded Geth, I have no idea, that is probably Space Magic on the part of the writers. We can't (yet) create an A.I. that complex and we don't (yet) have the mathematical formula to predict organic behavioral patterns (and perhaps Humans never will). But again my interpretation is that the logic, at least, is sound.
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The peace between the Geth and the Quarians is no different in concept to the peace between the Krogan and the Turians, it's simply one species or race agreeing to peace with another. So the upgraded Geth are just simply another "race", They may have slightly different cultures, and methodology, but they fit into the equation no differently than any other race or species in the Galaxy.
In the case of EDI, she seems to be trying to mimic "Humans" so she is perhaps eventually going to simply be a Human made from Synthetic rather than Organic materials.
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Having simulated emotions is not the same as being "alive".
As EDI states in an early conversation, she has a self preservation routine, and things that improve or facilitate that routine feel better than those that don't, so she tells the crew she "likes" it. So simulated emotions are merely a way for a "program" to be able to assign priorities and smoothly execute it's core functions.
However it takes several discussions with Shepard, and several programming upgrades to her core functions, before EDI begins to place a higher value on other things, and eventually other entities, and It's apparently not until the very end, when discussing why Shepard believes he can win against insurmountable odds, that EDI feels "truly alive" or in other words, human.
The Reapers and the controlling intelligence must also have simulated emotions. I imagine they must "feel good" when a Cycle concludes and "all life" hasn't been extinguished. They also must understand Organic emotions to some extent, as they are accused of running "terror campaigns" in or to help pacify and control organics to facilitate more efficient harvests.
But all of this is only to accommodate their core function which is to find a solution to the problem of these chaotic life forms constantly destroying themselves.
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As for the Control Ending dilemma.
From my interpretation of what the Intelligence has derived from it's equations, it eventually boils down to simply - the controlled will inevitably surpass and/or rebel against the controller.
So even though you may think that you, as the Shepard Entity now controlling all things, is simply THE greatest thing since sliced bread and totally incorruptible, the rest of the Galaxy may not think that, and in fact they will eventually rebel against your control.
So you will have to either a) relinquish control or
tighten your control.
Relinquishing control simply leaves a gap for yet another controller to fill (TIM would dive right in there) and the cycle simply starts again with someone else
Tightening control turns you more and more into what the galaxies inhabitants would consider a despot, and turns those same inhabitants more and more into mindless drones. (Hello TIM)
Either way, rebellion and/or destruction is inevitable.
And this is the point and/or central "theme" to the whole "Reaper Threat" story arc that the Bioware writer/s were aiming at.
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At least that's the way I interpret what is being shown to me in the games, you may very well see it differently.
Do I personally (in R/L ) believe any of it? Well ... maybe. It does has some validity (and empirical precedent) and the concept does have a certain "elegance" to it, But I guess I like to be more of an optimist (like Gene Roddenberry) and hope that we, as a Species (and maybe aliens as well?) will evolve past this. (the Synthesis ending
)
... but then, after all, this is what makes us individuals and "human" right? 