I would agree that the writers tip the scales in favor of the geth somewhat in ME3, but I think that's partly because they figured that people already had some sympathy for the quarians. I seem to recall a YouTube video of the 2012 PAX panel where someone from Bioware said they figured most players would instinctively side with the quarians if forced to choose and therefore they thought they *needed* to go out of their way to let the geth plead their case.
Personally, I think both sides seem to have done some pretty horrible things in the past. If Tali's version of the history is accurate, the quarians tried to shut down the geth *before* they ever showed any sign of violent resistance. They correctly recognized that if the geth were sentient, that would make them little better than slavemasters, but then the quarian leaders tried to kill them or at least put them into indefinite stasis rather than face the implications of the geth's evolution. That said, as has been pointed out numerous times, the quarian death toll suggests that the geth must have used some pretty indiscriminate tactics to fight back and have kept up a hostile isolationism since then. I don't think, however, that Legion is to be seen as a total anomaly but rather as the first instance of the geth finding a potential partner in organics. If you drop the firewall to let him communicate with the rest of the geth during ME2, his attitude doesn't seem to change at all afterwards, and he reported to Tali that they were having difficulty achieving consensus before the quarians attacked.
If I absolutely *had* to choose between the two in the context of the Rannoch arc, I'd choose the geth simply because they were, by all accounts, minding their own business and building their Dyson sphere when the quarians attacked them, and when the Rannoch Reaper dies and they are freed from Reaper control, they stop firing, at which point Gerrel wants to kill them anyway. But as is often the case in the Mass Effect universe, this doesn't seem to be an inevitable clash of civilizations but rather the product of short-sighted leadership and hasty decisions on both sides. Koris and the Civilian Fleet didn't want to attack the geth in the first place, and the geth only allied with the Reapers after the quarian attacks diminished their collective intelligence, while the behavior of Legion and the liberated Primes suggests that there wasn't a true consensus and that dissenters were simply outvoted and suppressed.