I think I'm going to play the Brotherhood of Shinsei, with affiliated monasteries and vast armies of fighting monks. I think they're highly underrepresented in the Rokugan setting, and were an important part of Chinese and Japanese history. However, I probably would not have much in the way of contiguous territory, as my monasteries would be scattered all over the place.
I should also have special rules that protect my units from random attacks by members of the Great Clans, kinda like the way the Bene Gesserit can co-exist with the Great Houses in the Dune boardgame.
Also, I think I should subsist on a tithe of IR from the other Great Clans, representing all the Samurai that eventually retire and join the Brotherhood. Perhaps all the Clans can expend a certain amount of points to change the political conditions so that they no longer have to tithe to me.
Rob