well a clan system is already here^^ http://blog.warlight.net/index.php/2013/09/website-update-2-2-clans/
It makes sense to me that the clan leader (and managers) from both clans agree on the settings, they an ofc talk to their clan members, so everyone would be included. I`m Imagining some sort where clan A challenges clan B, then clan B can either accept, decline or send back a challenge with different settings. (maybe using the mail system or smt similar would be good for this?).
A clan war IMO should be more than 1 game, I`m thinking it will be awesome if it could be made as a tournament where you don\t have to fight your clanmartes (obviously).
Maybe making a clan ladder, so the clan fights for points, will be a good reward system?