Without reading most of the thread....
The Geth in ME2 are NOT the Geth of ME3.
The Geth of ME2 only had contact with a Reaper mind. And most of them rejected it. Some of them left. Those were the Heretics.
The Geth of ME3 were facing destruction at Quarian hands (due to a logic bomb ambush). They either called out to the Reapers, or accepted a Reaper offer to 'help'.
This Reaper help was in the form of a code upgrade, making the Geth significantly more advanced than in ME2. I'm not gonna say they're like EDI, but they're at least more comparable to her.
The difference to the Geth must be enormous though. Able to form much more easy 'individualism' within a platform, and create 'life' that makes the Dyson Sphere look like nothing (in that and a few other respects).
The downside was threefold:
1)IT WAS A LIE. The upgrades are real, sure, but the Reapers' offer was not. The Geth are seemingly an insult, or at least an insect to the Reapers, and they took control of all the Geth. It seems that they used Legion/GethVI, the most 'individual'/separate of the Geth, in order to transmit the control signal (Legion wasn't totally necessary, but was on hand).
*Even if I'm wrong about it being a lie, the Geth still gave themselves up as 'slaves' to the Reapers, in order to survive. Survival was preferable to extinction, to them.
2)With more individual capability, a Geth platform may feel attachment to their existence as one. Less consensus, even while there is still networking. Likelihood of Geth 'individuals' disagreeing probably skyrockets, for better or worse.
3)These Geth pretty much betray all their goals of ME2. They got a taste of transcendence and want more. Or at least, Legion wants more. And he's seemingly willing to try to kill Shepard (Rannoch mission) in order to get it for all Geth. That can be deemed a betrayal to the whole war effort - an ally thinking in such long-terms, even as the Reapers reap the galaxy.
So you have to make a choice.
-Let the Quarians die, for the sake of the Geth and/or their Upgrades? With Legion this is more optimistic, but with GethVI it's made clear that the Geth will not take kindly to organics after the war.
-Let the Geth die, for the sake of the Quarians' revenge? With Tali (especially a Tali who becomes friendly towards Legion and sad for his death) this is much more understandable, but without Tali it feels like you've settled for the lowest-tier reward.
-Possibly try to cause a Peace between the Geth and Quarians, despite the risks that may be involved. Javik can explain a similar situation where the synthetics took over.
There is no way to have peace between non-upgraded Geth and the Quarians. Why? Because that's what everyone would shoot for. This game is supposed to be about some *tough* decisions for the playerbase. What looks like utopia to some, is terrifying to others. What looks like brutality to some, is pure to others.
What you pick may be guided by your own morals (even metagaming might count in that). It defines part of your journey towards terminus.