Here's what I'm thinking:
1. Missions are an alternative RP line to the basic Fight/Invade/Defend. They serve as guidelines for the characters to enjoy the world with a different purpose. The system is just that, not a way to gain something, just a way to experience the NW in a different manner. Unless what you guys are proposing is just another way to get rewards. NPC's can be invented at will, which can either be passive, aggressive, etc. They don't really have to be human, a mission could be simply to catch a missing cat, for example, or to hunt for a mysterious beast in the forest.
2. Missions should be handled by the Kages. We can give a set of generic missions that will entail either traveling inside one village or across to other villages or landmarks. People will have to RP their characters into the 25th Landmark of every village, which is the Kage Mansion, and in character request a mission to either the Kage or someone appointed to be the mission master. As mods we can provide an initial set, but the point is to be self-sufficient, and have a thread for people to submit ideas for missions for their Kages to approve and then give out. Inactive Kage that are unwilling to do this should be replaced.
3. Every once in a while, Mods could create special characters, or give permission to some people, to handle a mission. These would be requests where, in character, someone would go to one or multiple villages, and give out a special mission, that can be accepted or not, but will generally entail something more special than the average mission. This could range all the way from villages asking one another for sets of missions or joint missions, such as setting a trade route, helping with a problem, etc. The idea is to solidify the relationships of every village and even with select missing nin. If two villages don't get along, missions could be handed to ransack or steal or spy. If two villages do get along, one could be doing missions for rebuilding the town, escorting a VIP, etc.
4. I like Pervy's idea of doing missions in order to get permissions, and I will implement that as well. So now you have two Mods that will give out permissions if you request a mission from your Kage and then complete it. Punctual rewards can be given in special missions. And if someone is doing quite a lot of missions, and doing them correctly, the Kages could request us to allow certain prizes so that they can hand out a special mission to the deserving member. So, rewards can happen, but they will not be the focus of this mission system. Do you want this, or not?
kun: