a Mary Sue character that makes the setting crappier just by existing
You gotta admit, Mary Sue characters who make the setting crappier just by existing are staple parts of the L5R storytelling ever since the very beginning. So for one, Daigotsu is cool this way, and definitely better-off than Hida "I razed the Empire to the ground at the head of a Shadowlands army and they turned me into the fortune of perseverance" Kisada.
Seems we're back around to the "major events that have no consistency with the setting out logical follow-up" thing?
Meh. It is just L5R Storytelling 101. You can't talk about anything in the canon without running into the usual circle of inconsistencies/Mary Sues/silly stuff/whatever that makes the setting "crappier". I mean, these things almost define L5R, and without them, the setting wouldn't be the same.
I'm not saying your wrong, by the way (you're certainly very, very correct). Can we also apply moto chagatai to this list?
Definitely.