I think the problem was that most of the devs just wanted to tell the N'Zoth story, but they got forced to add that weird pvp plot on top. And when Afrasiabi left it was already too late as stuff like the Sadfang Cinematics aswell as the pre-patch / first patch would already have been in production/finished. N'Zoth was clearly the endboss from day one (the Aszhara video made that clear, as did Alliance questing).
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We can only hope that being free of that creep will help the current writers to tell the story they want to tell. We can only judge once Dragonflight comes out, but it looks promising already =)