Some of the most interesting and dramatic events in feudal Japan arose from disputes between the many religious factions and institutions- individual temples as well as schools of Buddhism competed vigorously, sometimes viciously, for influence over both the aristocracy and the population at large. L5R tends to present Shinseism as more or less monolithic, with the exception of the Pure Lands movement, which is somewhat understandable given that Shinseist doctrine is never developed in any great detail. This leaves room for a lot of fun and interesting development within the setting- competition and conflict between Shinseist monks and/or Fortunist priests on both the political and ideological level can be a great way to involve samurai PCs of many different sorts, since the instigators are "neutral" with respect to the Clan system of Rokugan.
I'm curious if anyone has made heavy usage of sectarian/ecclesiastical politics in their games, or brought the fine points of Shinseist doctrine into play in a material way. I have more thoughts on the topic but would like to hear what others have done or thought of first!