We're trying to make Planetwars more inclusive to non-clan players, allow everyone to contribute in a meaningful way to the outcome of Planetwars, and lessen the total dominance of the few small very organised clans.
There are 5 factions, and everyone is in a faction, whether they're in a clan or not. This means whenever you play you're contributing to the overall conflict and the success of a faction that actually has a chance of winning (rather than the dozens of 1-5 man clans that never have a hope).
Clans will exist within factions, can contribute to that factions success, and will be balanced to be on the same team. They will own and control planets. Factions will tend to be balanced to the same team, but intra-faction battles are possible (which decide which clan holds a planet, rather than which faction does).
Factions serve basically like a large, fixed alliance would now- primarily they are shared victory conditions. They are not like races or factions in an RTS (or factories in Zero-K) where each has different powers and your choice determines which power you get. That would probably make one faction better than another or make people displeased about which faction they're placed in (Since some of it may have to be automatically assigned to assure balance).