Soul Society really should never have stopped being villains because so much about them is profoundly fucked up and once they become allies they just forget about how fucked up SS is even though there's no reason to believe they've changed and several to believe they're a shitty as ever.
It also, admittedly, really hurts the thematic underpinnings of the series.
Ichigo and friends versus the Soul Society, with Byakuya as its avatar, is (for Japanese kids) a very relatable story about youthful rebellion against a stodgy, conservative system that commits casual atrocities in the name of decorum and tradition. It's teenagers standing up and saying, "Wait, letting your little sister die to uphold the laws and dignity of a crumbling system isn't 'honorable' or 'noble', it's fucking stupid. Change the system!"
It's doubly problematic because it's not like Aizen is the secret architect of all of Soul Society's faults. He's, if anything, another rebel trying to bring down the broken system. So the core conflict of youthful idealism versus regressive conservatism never really goes anywhere, everyone just gets distracted by this
other guy who's doing the
wrong kind of rebellion. Oh, and Byakuya learns to be a little less of a douche, but the actual Old Guard in charge of Soul Society never do and none of their system ever really changes.
Even with the end of the series, it's not like they really learn and change. They just find a different blind, maimed god to use as a lynchpin.
(However, in terms of shit swerves, it doesn't even hold a candle to Naruto becoming the story about how the only thing that matters is who your parents are and what genes you have. There's really no contest when it comes to shitting the bed on theme.)
