I think one important point has been raised - big bad introduced early. THAT has been the fault of many of the less memorable arcs - the Big Bad coming in too strong, too early, and then just bogs down into more of the same waiting for the story arc to end. Iuchiban and Kali-Ma readily come to mind. Kanpeki may well have ended up being more of the same if Onyx had gotten off the ground.
The best "Big Bad" story arcs (Imperial, Gold) had the big bad maintain a lot of mystery as to their identity and goals for at least half the arc - they sowed discord and weakened the empire in preparation for their master stroke (taking over the empire as Hantei XXXIX/Releasing Fu Leng to assault Tengoku).
It,s okay to have a big bad, but in a setting like L5R, you just can't have the Big Bad keep up momentum for an entire story arc like Iuchiban or Kali-Ma would have needed. Not with story tournaments getting in the way - once the Big Bad tip their hand there WILL be a rallying effect.
Edited by Himoto