It did seem to be shifting in ME2, though. You had Koris advocating leaving the geth be, Xen insisting that the geth should be subjugated, and of course possibly having Legion put a more sympathetic flashlight on them, dispelling the idea that the entirety of the geth supported the reapers.
I was thinking of how they presented Quarian characters in general in ME2.
When interacting with another race like say the Asari, the player knows Liara, meets nice characters but then also encounters all sorts of galactic refuse. There is a coldblooded killer, a corrupt diplomat who later becomes a villainous corporate executive, a sex vampire mass murderer, a corrupt SPECTRE, slavers, a sleazy contract lawyer, and of course countless thuggish mercenaries. The player kills dozens of them in combat and executes several others as well. You see the good and the bad and that's just fine.
In contrast, Quarian characters are almost always victims that the player saves or a damsel in distress that the player will whiteknight for.
You save Veetor from torture at the hands of Cerberus goons (You can turn him over but the game makes it clear that it is the wrong decision).
You save that Quarian girl on Illium from her predicament with the slave broker.
You help out a Quarian girl on the Citadel with the comically racist Volus and obnoxious cop. This could have been an actual ethical dilemma if she had taken the money but instead it is just about yelling at some bigots on behalf of a damsel in distress.
You save the Quarian on the jungle world from being eaten by dogs.
You save Kenn on Omega from the elcor's extortion.
There is of course rescuing Tali multiple times as well as saving Kal Reegar.
It's obvious what BioWare is doing here. These situations work to engender sympathy in the player. Even the worst Quarian in the game is an extremist instead of an outright villain and there's the emotionally charged justification with his daughter. The Paragon (read as correct) option is to cover up his misdeeds. There aren't any unambiguously bad Quarians like there are for the Asari with Nassania Dantius. The player also never even fights Quarians in combat, kills any, or plays through a plot arc where one is a boss or antagonist. It's a little odd given the good and bad we meet from the other races (or just the outright bad guy stick the Batarians and Vorcha are hit with). Perhaps it is damage control from BioWare to shore up the Quarian's position with players vs. ME2's new Geth?
In the long run, it probably would have been better if the game had focused less on being the knight in shining armor and more on actual issues with the Quarians like the strip mining or extortionate behavior mentioned in the Codex or ambiguous situations like if that girl had actually stolen the money out of need. Perhaps the Quarians could sometimes "take" ships? It would add depth and the player would be shown (not told!) their desperation.The Migrant Fleet is dying and they're having to resort to increasingly morally dubious measures to survive. Given later events in ME3, it would help support their case for retaking their homeworld with players.