And I think you can have that with or without a questionable person on the throne, actually look at the history of L5R, the Clan War which is so beloved by many that they want to reset the satting to that time basically had the same premise, a questionable emperor. So, L5R can tottally work that way. They don't have to frame it as a good vs evil conflict
The Clan War is very different from what I understand Onyx Edition was going to be. I mean, maybe I have something wrong, but the Clan War was basically the Crab rebelling, everyone else going "Whatsa matta for you, Crab?", and the Emperor's corruption being revealed much later. But the story assumption going in is that the emperor is the true light of heaven, never wrong, spoke ex cathedra, and all that. That he's been corrupted (or possessed or whatever the details were) was a big reveal, right?
By contrast, I understand Onyx to be much more, 1000 years of darkness, Emperor explicitly evil and everyone pretty much knows it, etc. Much more like Star Wars, actually, where even a cursory glance at the Empire makes one go, "Yep, bad guys." Right?
Those are two very different things.
With the scorpion coup it was early on clear that there is something wrong with the imperial bloodline. And it have not just been the Crab that rebelled, almost every clan felt free to ignore the emperor, since he was weak and nobody trusted Kachiko who spoke most of the time for him. It basically was exactly what Onyx could be, a nation in which the clans fight with each other and nobody really cares what is happing in the capitol. So, I want that weak and ignored emperor, who sits on the throne but has no power and the clans do their own business without involving the imperials much. That could even leave the Spider as playeable faction, who try to get more control over the land they officially already should have. That is inherently a rich and living setting with a balance that is interesting, not so weak sauce we get with all those benevolent emperors who just make idiotic decisions (Sorry, but AEG had at least an excuse for Toturi with the lying darkness, but Nazeru and Iweko have just been terrible on the throne).