Honestly, the writing kind of fell apart during the whole Rannoch climax.
I wouldn't be the slightest bit surprised if the writers just forgot about that stuff.
After all, remember how adamant Legion was in ME2 about how the 'true' Geth should develop their own path seperate from the 'old machines'? Unlike the heretics who accept the gifts of the Reapers? Yeah... not any more! Reaper code for everybody!
I also loved Legion's explanation for why he wasn't under Reaper control like the rest of the Geth. "This platform is too complex". Yup. That one reaper was controlling the countless billions of programs comprising the Geth collective, but apparently Legion was just too complex for it. (Bear in mind, the only difference with Legion is that his platform houses more programs than the normal ones so he can remain intelligent even when out of contact with other Geth.)
The whole Reaper upgrade kinda "ruins" the Geth if you ask me. They were interesting because they were so distinctly other, with their collective intelligence and synthetic perspectives. Add some Reaper code and BAM, suddenly they are "truly alive" ('cause they were dead before that, right?) and talking in first person and shit. The things that made them interesting are gone. Luckily, we didn't see much more of them after Rannoch, so the game never got a chance to really rub it in.