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Speaking of simpler evil plots...
I think it's reasonable that Sephiran chose to go with the world war route instead of the galdr route, since at the time he went a bit mad, he thought the apostle was dead.
What's strange is that he decided to enable a distant relative of the throne in Daein to do so before taking power in Begnion. And, after having power in an angrier, bigger country, he decides to use his country to keep the peace while setting the stage for a bigger uprising in the continent several years later.
Um.
Considering how close he was to Sanaki's heart, and how racist the senators were, it would've been a hell of a lot easier to just make Begnion start shit. After all, someone in PoR says that if Begnion sided with Daein, then all the laguz countries would quickly dogpile onto Crimea's side and bam, world war! (I think this was suggested in the laguz cutscene? I think it was mentioned somewhere else, too.) Really, a country with Begnion's prominence would have a lot more resources to embroil the world in war, and I don't think the senators would be against that idea.
My personal conclusion here is that Sephiran is a softie and couldn't (and never did) use Sanaki like he did Ashnard.
Aside from the senators' removal of Sanaki from the political scene, which I think was out of Sephiran's control anyway, and Sanaki's endorsement of Crimea's cause in the first war, I can't think of any way Sanaki played a role in Sephiran's plots. (And Sanaki likely would have reacted the same in both situations with or without Sephiran's direct advisory.) If he manipulated her in any way, he manipulated her by raising her to be as strong-willed and righteous as she is, which isn't ... genuinely manipulative.
Did Sephiran originally intercede in Begnion to gain political influence there for his schemes? Did he change his mind upon getting to know Sanaki? Was that arc never part of his grand plan at all?
In any case, his lack of exploitation of Begnion seems to me to be further support for the genuineness of his relationship with Sanaki.

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Yeah, the inequity between Zelgius and Sephiran is really quite heart-wrenching. Zelgius dies with Sephiran on the brain, but after that you don't hear Sephiran talking about Zelgius even once.