Maybe instead of clans there could something similar to this, with only like 3-4 teams of course. (tl;dr ex: There's 10 teams, and then each will need 10 managers w/ 1-2 back-up managers for each team (we don't need a back-up with our small battling community). Then, when every team has a manager chosen, there will be an auction to bid on battlers that have signed up (this is can be changed as well). And there will round robin style playoffs where each has to face each other, etc (like clan wars pretty much).
Good thing about having an auction for choosing battlers (or something similar), is that it prevents everyone from just joining the team DA is in, etc. It also keeps the good players balanced out, so they aren't grouped into one team. I didn't read the entire thread thoroughly, but that was just the general I got.
Having clans like this could prevent less spam since they would be more moderated and such, and random people wouldn't be able to make bad clans (spam pits).