If all shukenja are good, this reflects on the oriental situation for deities. These theories might resolve the issues. Each is presented as an option to be applied to certain deities or within specific geographic areas.
The mix would vary by alignment, with good gods having the most shukenja, evils the least, lawfuls the most sohei, chaotics the least; evils the most shamans, goods the least (shamans tend to be very self-serving, frequently power-grabbing or opposing tribal authority); chaotics the most unattended shrines, lawfuls the least. Clerics (druids) would be few in number, centralized at the most significant holy places, and absolutely parochial, possibly monastic, regardless of alignment. Sohei could take on some priestly duties at smaller lawful shrines, possibly some neutral-ethic shrines, in conjunction with their protective aspect.
The mix could also vary by the character of the specific deity. Gods of war would utilize more sohei; gods of health, luck, and fertility more shukenja; gods of freedom more shamans. Some gods might use none of one or more types. Others might so emphasize one type as to dwarf the significance of all others.
The decision should be made for each deity activated in the game. Players should be made aware of what type of holy men serve his god; and if his character is known to oppose a particular god, what generally is the type of servant that god might choose. Note that many gods might blur the oriental/occidental distinction, requiring consideration of who serves the god on both sides of the divide.
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Combinations of these solutions may be possible. A deity might have a handful of clerics (druids) as a temple hierarchy, plus a few odd wandering shukenja of similar ethic dedicated to him, plus other shukenja serving other gods but able to reluctantly perform service for him, plus many shamans scattered through villages and among wandering tribes with various theologies related to him, plus numerous shrines and temples at which no one officiates but worshippers congregate.