Huh. Odd that my discussion with Collider would catch on now of all times. Glad to see we're not trolling.
I'll go ahead and repost my last bit from last night, with a few edits.
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I don't think that the quarians prejudice against the geth is wholly unjustified. I disagree with it, but I understand the circumstances and I can see how it would be hard to feel sympathy for the geth from a quarian's perspective. However, I do feel that the quarians struck the first blow and, if I remember correctly, Tali in ME1 even classifies it as such (and most of Shepard's responses also see it as such). The intent behind the quarian deactivation of the geth was not to "assess" the problem and begin a dialogue between the geth and the quarians. It was to prevent a species from coming unto its own and challenging their authority.
I can understand the interpretation that the quarians simply were trying to diagnose a technical issue and that the geth overreacted, but I disagree that the quarians' intentions were not genocidal, at least in some sense. If you press Tali in ME1 on the issue, she'll simply say that free-willed synthetics and organics are incompatible - that peaceful relations are simply impossible between the two. She even goes on to say that, should the quarians have attempted to form peaceful relations with the geth, they would have been left with other problems, such as having a large slave population that might want rights and, of course, sanctions from the Council. These don't sound to me like attempts to deflect the charge of genocide, they sound like attempts to justify it.
Again, the circumstances of the Morning War and the incredible death toll the quarians suffered make Tali's (and most quarians') response understandable and sympathetic, but they don't make it any less blind or one-sided from my point of view. Granted, few in the ME universe are willing to accept peaceful relations with any form of AI, but widespread prejudice does not justify prejudice from an individual - it is wrong regardless and both EDI and Legion demonstrate that AI need not be at odds with organics.
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On another note, it occurs to me that Xen might end becoming a major adversary in ME3, given the hints dropped in ME: Ascension that the quarians were going to try and use the reapers to control the geth. Of course, that plot thread might be completely abandoned, but I'm hoping it won't be. It could be a very interesting route to take with the story.
If it does happen, I'm guessing the Tali/Legion confrontation or your solution to Tali's loyalty mission will come into play. Xen and the quarians as a whole might try to use the technology or, if you win the loyalty of the quarians, she might end up leading a rogue faction.