I think you should have went the other way with the banner balance. The problem shouldn't have been seen from a faction/clan perspective, but from the one man pubber's perspective. Factions were already rolling servers with banners, now only the actual members will be rolling the server, making it even more unbalanced. It actually balanced teams out some when you get some random noobs who throw on the faction banner to counter the "pro's" in the faction.
I think you should keep your new "pay for banner slot" idea, however I think you should totally change the way balance in public servers works. You should try to keep people balanced by banner (when possible), however you should balance by class/equipment selected, skills, and either something like current K:D ratio, win:loss ratio, or overall k:d ratio (or even better, damage dealt:damage received ratio either short term or long term).
I think you'd still be able to balance most of the banners together with that algorithm, but I'm tired of teams being stacked in public servers. I say this as someone who routinely enjoys having the most people on with our banner in the NA1 public battle server. It seems like Hospitallers always have the most people on, and we're always getting x5's. I'd rather have even teams (and still play with our faction members, but only if the teams are balanced first).
