Indoctrinated against their will more or less, and moreover they are individuals instead of members of a networked collective intelligence, so their decisions do not necessarily represent a propensity for their species as a whole to willingly engage in psychopathic, violently destructive tendencies.
Two points regarding this:
1. Neither character began as indoctrinated. Saren in particular joined Sovereign via free will. In other words: he was willing to put all of civilization at risk on the promise that he (and others) might be spared. Sure, you could argue that Saren's loyalty was enforced down the line, but had he never taken that first step, Sovereign wouldn't have had the chance to indoctrinate him. He knew exactly what he was doing at the start.
2. And note that this one organic in this instance had the potential to produce galactic genocide because of his decisions.
Putting aside of course that not all synthetics operate on the same parameters as the Geth (Ex: EDI).
They would've be exterminated by the Reapers after everyone else was reaped regardless, so "survival" is a......retarded motivation to say the least. The geth stood to gain nothing and lose everything when they could have easily retreated in the face of defeat (you know, like the quarians managed to do 300 years earlier). Stop defending and falsely categorizing it as something organics would do, because not a single other species willingly turncoats to the side of the Reapers to help them in their objectives for any reason. You have no evidence of that being "likely."
You're right. It's not likely, it's guaranteed. Case in point? Saren, who made this exact argument with regards to submission vs extinction.
If you want to point out how desperate the idea is that the Reapers would grant a repreive for support, you'd actually be on the money. But it's not exactly uncommon for characters to take desperate actions, under threat of death. You should probably factor that into your calculations, given that ME1's premise relies on this.
f anything Mordin prevents a genocide, either of the krogan by perhaps less benign species who would simply go all the way rather than messing about with fertility rates, or of whatever the krogan would inevitably do to their victims if allowed to expand unchecked.
No argument on Samara, she's absolutely cuckoo just like her daughter, but again an individual who doesn't reflect on the species as a whole, and her goals aren't galactically destructive anyway. We only ever see or hear of Thane killing horrible criminals. There's not enough information there to compare him with any of the AI's who seem to indiscriminately slaughter every organic they come in contact with when it meets their objectives to do so.
Well, Mordin doesn't see it that way, especially since it was the Salarians' fault in the first place for uplifting the Krogan because of their own conflict with the Rachni (Mordin's Example: Giving nuclear weapons to cave men).
Regarding Thane, his own dialogues disprove this interpretation, specifically in regards to how he met his wife. This is essentially Walter White rationalizing at play.
What strawman? Synthetics who aren't controlled by and don't kill organics en masse are in the extreme minority in the ME universe. Conversely, organics who kill organics en masse are in the extreme minority. That is backed up by simple arithmetic and isn't up for debate.
Our "sample sizes" amount to EDI and the Geth. The former has been exclusively helpful and the latter simply acted in defense of their lives, once genocide was initiated. And note of course, that the Geth themselves managed to decide to pursue an alliance with Shepard, without any sort violent intent towards organics in ME2.
Not to mention, your own Quarians were responsible for attempted genocide once they realized the Geth were gaining sentience.
Your expectations are irrational then. It has happened before with one and not the others. The AI even frequently makes jokes about killing organics, which is totally funny considering it has. Moreover, you have a good idea how human thought processes operate, but no idea how AI process do, nor any means to anticipate them. EDI can kill every living thing on the ship before they even know what is happening simply by cutting life support on the flip of a quantum bit. Ashely or Kaidan can't unless everyone decides to catch the idiot ball at the same time, nor have they any motive to beyond sudden onset of psychopathy.
Do I? Because I seem to encounter a plethora of humans who don't mind causing large scale destruction on their own. Saying "Herp derp you don't know what EDI will do!" doesn't really amount to much, particularly since ME3 does emphasize her value as a companion, to say nothing of all the terrifying ideas put into effect by organics (Mordin's Genophage, Shepard's Relay in the Arrival dlc).
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