Endwalker is the most controversial expansion

[Absimiliard]

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You seem to be conflating the Garlean people with the Garlean military/government. You're also rather handily forgetting that the vast majority of Garlean military personnel were in fact conscripts, and that a lot of the not so great things they got up to were being perpetrated by said conscripts.

To the subject of the EE: A few key details:
1.) Nael, who had as mentioned before been directly responsible for keeping the project alive in secret, in fact lied to the Emperor by claiming the weapon could now be controlled.
2.) Note the aforementioned cleansing mentions only beast tribes and eikons. The beastmen, barring a select few (who the Garleans had no knowledge of anyway), were believed to be tempered to the last. This particular point comes up in-game on a multitude of occasions. Solus and Nael aside, all participants at this time believed it could indeed be controlled, which means we can readily infer the general intent was not to obliterate the entirety of Eorzea.
3.) Only Emet-Selch, who we now know was Emperor Solus, and Nael knew what was really inside Dalamud. Everyone else was completely in the dark.
4.) Obviously, Emet-Selch planned all along for Bahamut to be unleashed at the appropriate time. It was always going to happen, and not for the betterment of Garlemald. It was all for the Rejoining. They lost a lot of troops that day.

You may also note that, at that time, the beast tribes were for the most part not regarded as intelligent even by the Eorzeans. They were seen as hostile servants of primals at worst and dumb animals at best. It should go without saying the Garlean ruling body would hold a similar view of them, as they had no reason not to.

The Twelve were regarded as nothing more than eikons by the Garlean Empire. Much of the Ala Mhigan's culture revolved around their worship of Rhalgr, including their rather violent past. Despite this, they were still allowed to retain a fair bit of their culture. Other regions they'd conquered seemed to have remained relatively unscathed from a cultural perspective, though it's fairly likely these areas placed far less emphasis on eikons.

Anywho, to tl;dr it: I strongly disagree that the Garlean people are being handled with due sympathy in Endwalker. The Eorzean Alliance is going about "helping" them in a way that comes off as extremely predatory and ill-intentioned. I further disagree that the Ala Mhigans are in any way sympathetic, given the atrocities they have knowingly and willingly engaged in.

Now, with all this being said, we've gotten waaaayyy off the original topic. None of this has anything to do with Endwalker being controversial, but the fact this thread has garnered a fair amount of attention does kind of lend credence to the idea it was.