1. Being able to create your own member rankings, rather than the default Member, Elder, Coleader
You could create up to, say, 5 different ranks, with each having any number of abilities, such as:
Inviting People
Kicking People
Promoting People
Editing the Clan (Flag, Description, etc)
2. Being able to initiate Kick-votes
This ties in to #1. Lets say you want your medium level members to be able to request someone be kicked. Thus, they could initiate a Kick-vote, and if the required amount of up votes is reached (set by the leader) then the player is kicked.
This could also apply to promotions
3. Having a better user to user chat system (Private Messaging)
This would make it considerably easier to have subsidiary (feeder) clans. It is much safer than sharing e-mails or phone numbers.
4. Having an Alliance system between Clans.
Again, this would make it much easier to have feeder clans. Possibly allied clans would never fight in Clan Wars, and could possibly help each other out (indirectly) in Clan Wars.
Or, taking this farther, you could set up a clan alliance hierarchy, in which some clans in the alliance are ranked above others.