Speaking of species, what about the Kitsu? The sharpshifter race that was hunted by Akodo and ended up a Family inside the Lion Clan? Yes, at the era we usually plays, Kitsu lost most of their abilities but they were another species, in the same type as Kenku, Zokujin, Trolls and Ningyo, which are the first five races of Rokugan.
Also, I like what Zoomfarg said about the: Use materials that you like it. I tend to prefer using some species as more than simple enemies, it creates another kind of atmosphere. Does it have to be "humanized"? Of course not, but they can have their very own complexity and their kind of morality. Which is why it's great to have guidelines on these species to have more than stats for skirmishes.
Do I want a L5R with human only? Of course not! Why? Because that brings another interesting aspect to the game. And that aspect is xenophobia VS collaboration. I have ideas of small RPG quest where a group of non-Crab have to collaborate with Nezumi to be able to archieve their goal. I say non-Crab, because Crab and Nezumi have a "good relationship" while the other clans sees them as enemies. Yet, in a common goal, collaborating with your enemies is a struggle between your values and the achievement to that goal. Where the Nezumi, as a temporary ally, may not understand very well some things and bring tensions between the alliance.
It's a very interesting aspect that is in L5R. Why remove it? Because Xenophobia? Because a few people are using them as standard characters and make them feel too standard? Yes, it may be poorly used, but why should this be removed simply for the few exception?