If I may contribute my two cents, I am quite new here at Test but had extensive experience with other social games, being part of an organized awesome community like this is going to be on the PU.
I have been part of a clan with roughly 1k members and there were a lot of subdivisions in it, each player was assigned to a brigade and each brigade had a forum section, one leader and two to three sergeants, the purpose of this subdivision is that it is very rough for a single person to manage and provide supporte for more than some dozens of players. There were also some offices where you could pursue a specialization, a war, intelligence, internal affairs, foreign affairs officer, but you still had a brigade and reported to your brigade leader.
I am not saying this is the way to go, but from my experience this structure provided a very good player experience for the following reasons:
1 - As soon as I joined the team I had one point of contact with whom I developed a relationship, he tutored me from the very basics to advance strategy to improve my gameplay, recommended me for promotions, etc... This was both rewarding from the learning perspective and on a personal level.
2 - Each brigade leader and their sergeants cared for their crew, knew each of them individually and the brigade members loved them and looked up to them as great leaders much better than the other brigades had
3 - We were pretty awesome, kickass alliance and rarely got into conflict because the others were afraid of us, therefore a healthy competition between brigades made for things more exciting, where we always tried to be just a little better for any goal that the leadership set for the alliance.
4 - The specialties of players did not separate them in groups, we were divided equally among the brigades making for a varied group where we learned about different trades with each other, but by the time we were mature enough we could apply for an office where we were expected to have a higher commitment and produce some kind of work depending on the specialty we chose, but we still were a part of our original brigade. When I held a position in the office of internal affairs and afterwards war, it was really satisfying the feeling that i was contributing to make my alliance even better.
5 - It was fun going to the other brigade forum sections and teasing them :)