The CWC (clanwars contest) is similar to what you describe. There is a "council" of sorts, made up of delegates from some clans, all hand chosen by the tourney director--Tomisama.

Although I can initially see the intellectual appeal of a unified clan council, I don't really see the need for it in the tourney scene. Most of the time we just debate the rules or whatever and come to an agreement anyway.

As far as I know ther havent ever been any major disputes at the CWC, and it seems to work great. There are seasonal qualifiers and a year end competition, just as you suggest.

Go check it out:
http://www.clanwarscomp.org/

I think you will find it is very close to your proposal, and also that Tomisama might be interested in your council idea.

I think the main problem with your idea is that most clans just want to compete, they dont care about administering the tourney. It would be hard to get enough active clan representatives to make the council a meaningful ruling body.