They still allowed plenty of room for ambiguity and it wasn't nearly as one sided because it didn't attempt to retcon any other lore via a biased, propaganda esque presentation (it simply introduced a new element, the Heretic-Prime geth split), though yes the pinnochio "soul" nonsense was introduced in that game.
I didn't find it one-sided, to be honest. The only thing that could lead to blame the quarian is that They started the attack when they knew the Reapers would come (Which was indeed moronic, but not worse then the Geth volunteering to be the Reapers' slaves).
Anyway, If not for the third choice I'd had a hard time picking one, so If their goal was to lead people to pick the Geth, it didn't work on me.