Welcome to my playthrough of the multiplatform sensation that is Genshin Impact!
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We're coming full circle with this. Back then the set up for Inazuma was that Ei had been running the nation into the ground. We got several admissions and improvements here. First we got Ei admitting that while she had claimed she knew everything going on outside of her Plane of Euthymia during the Archon Quest, that she knew nothing and now she was feeling the consequences.
Side Note: This simultaneously also explains how she's not quite the Archon that real Archons are. For example Nahida was literally trapped inside of a "euthymia" and for exactly 500 years, longer than Ei put herself into that consciousness plane. Yet she knew everything that was happening in Sumeru to the point that she was even possessing those afflicted by the Divine Knowledge Capsules, using them to help her nation. She also entered into people's dreams to help them.
Additionally, the Shogunate had previously exiled most of the youkai from territories they'd allotted to humanity. This was the story we got from Itto's Character Quest where the Blue Oni fled while the Crimson or Red Oni tried their best to acclimate to human society. (in fact watch until the end because we get an update on that too)
Then of course there's the Chiyo thing but that didn't quite play out in a meaningful way. All in all it seems like Yae's playing the long game. She knew Inazuma had been going the wrong direction since the Shogunate took over but she lost so she couldn't really do anything about it. Not until the "winds of change" arrived anyway. But she knew Ei's stubbornness would flare up again if she tried going all out to course correct