Xeriar said:
I've been away from Rokugan for a very, very long time, but the Kitsune and Kenku have not been wiped out, have they?
Not wiped out. But they've never been a factor in the Empire. Kenku tend to be neutral, reclusive and even in the really bad times had nothing to do with humans outside of an occasional lesson. Kitsune actually reside in the Realm of Animals, but can travel to the Realm of Mortals, where Rokugan is, through a portal on Fox Clan lands. They tend to be CG, and thus are slightly on the villainous side in Rokugan.
Not to say that there aren't nice people in the land - even Bayushi Shoju was a good guy in his own way.
Relatively speaking.

He could be considered a tragic hero in that he was willing to sacrifice everything to do what he felt was necessary to save the empire, and ended up helping bring about what he had feared most.
I'm rather surprised that the Kolat and Shadow have no power - were they wiped out too?
If by the Shadow you mean Nothing/The Lying Darkness, it was 'destroyed' at the battle of Oblivion's Gate when it was finally given a name by the new Lady Moon. Some of the followers of the Lying Darkness remain, the Goju and Ninube, and both serve the Shadowlands now.
The Kolat have issues. They were crippled by Shinjo and the Lying Darkness. At the same time their purpose has been called into question. With the Sun and Moon replaced by ascended mortals, a Great Clan not founded by a Kami now existing, and the Hantei no longer ruling the empire, quite a few believe the Kolat have achieved their goals. Ahem, even if they didn't really have much to do with actually causing those events.

The Daimnyo of the Ox Clan is one of the Ten Masters, so they are still around.
Not to mention I only really followed things up to the Clan War, then lightly until the Spirit Wars... and nothing after. Let's see...
IMHO, the Four Winds story arc is the best they've done since the Clan Wars.