I sincerely hope that FFG keeps the story choices about things like "this clan decides it wants to ally with the Shadowlands and march on Otosan Uchi" or "hai guyz, we're all gonna try and go bloodspeaker!" OUT of player hands- because after over twenty years of AEG/WotC history, we've learned one thing: The playerbase as a whole almost never embraces transgression, while the individual players who do cannot resist doing it just be contrary. There's no plan.
As a Phoenix fan? I'm not just violently anti-maho to a knee-jerk and predictable degree due entirely to the crap inherited from before i even picked up the RPG or CCG, it impairs my ability to interact with players who actually LIKE the Phoenix dabbling in maho/embracing maho with both hands and doing a little Fu Leng dance. Every clan has piles upon piles of various story elements grafted onto them over the last couple of decades- FFG needs to be able to parse these for the story they need to tell without Joe Blow wandering in out of left field and going, "oh hey, these Shadowlands cards let me win, I'm gonna use 'em!" or, even more perversely, "I want the Crane to be oni-worshippers, so I'll kitbash a deck that uses as much shadowlands as possible and win that way, regardless of where the narrative should be going."
I've seen people bemoaning the fact the FFG's story choice options seem more limited than what AEG offered.
But considering that any reasonably sober analysis would indicate that AEG went too far in the other direction... I hope they keep control over that sort of thing.