The control is not what we're concerned about, if our clan got off the ground we'd either
A. find an unoccupied system to call home.
Or
B. Use Minor with your consent.
We're not powerwhores so operating from a system we don't own doesn't bother us.
We wouldn't make rules or take control, hell we'd probably help you enforce your laws, though we'd be conducting our own operations.
Most likely we'd only stay until we found a suitable system of our own.
As for the numbers
Put a limitation on it, like 5 or 6 clans to a faction, so people at least have a variety of clans to pick from if the slots get filled up.
Its actually not that stressful with the creation system they have going on.
If a faction is filled up and someone send an application to start another one, simply say "sorry, all the slots are filled" and do it in such a way that it doesn't seem like your saying "You're new here, in thus I'm better".
One clan per npc faction is just too one sided and really not all that fun.