Even the first season had Amon, the guy that wanted equality between benders and non-benders. At one point we're even shown that power was cut to a predominantly non-bender neighborhood, and when people went outside to protest to get their power turned back on, they were all rounded up and arrested. Afterwards, when Korra goes and tries to get the people that were arrested set free, she's told

All equalist suspects are being detained indefinitely. They'll be freed if and when the task force deems them no longer a threat.

Just in case it wasn't clear enough by that point that non-benders were treated as second class citizens.

I've been meaning to re-watch Korra, but I remember even the first time I watched it being a bit disappointed in the "enlightened centrism" where they are trying to paint every conflict as pacifists vs extremists.

I think it's similar to looking at BioShock 1 and BioShock Infinite. There's a lot of writers out there who just use politics and ideology as a setting for the conflict rather than actually being central to their message. It's simply a solid formula to make a villain: take any sort of stance and push it to violent extremes. Comstock is a religious zealot, Andrew Ryan I don't think ever even mentions spirituality if I remember. Ken Levine's message in the two games is not about religion, but extremes.

There are benefits. It makes the villains more nuanced and relatable. It gives the protagonist room for doubt and allows for some of the "good" guys to take on antagonistic roles. But Korra also ends up supporting an oppressive regime, and Booker DeWitt gets shoehorned into fights against the people rebelling against his enemy because... Reasons?

If you're talking about Kuvira you should read the comics that take place after the show. My feelings on Kuvira became much more mixed as I ended up sympathizing with her after finishing them.

They also try to get rid of the avatar, because she is an infallible being with incredibly outsized power.

Did autocorrect change "fallible"? Because otherwise it makes the opposite point.

Even in the first season, I was siding with the equalists :s

I think what made that group such good villains is that you could definitely see their point of view. That said, they left behind a TON of collateral damage, and they didn't seem to care that innocent people, including children, died in their wake everywhere they went. They were terrorists that happened to have a noble cause.

The formula for a good villain is "legitimate grievance, insane solution."

No they definitely were bad guys. You cant try to murder someone just because they were born as a specific person you dont like and be good guys. And they didnt differentiate between the Earth queen and any other ruler. Their ideology when it came down to it, was indefensible trash.