In general, 2 permissions for structures at a whole. And then define which actions take which permission setting by default to make use of 1 block per activatable less often required - less annoying.
two levels of permissions, or two permission blocks? You need probably hundreds of them on a structure, you don't interface with them (they have no gui) and faction permission modules allow anyone from the same faction to interact with blocks touching the faction permission module. Public permission module works the same way.
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Things are usually stolen by low-ranks who have been planted into the faction, either by a solo player or an opposing faction. When things get stolen by a high-rank, it's usually an intrafaction issue that can be resolved internally. If the issue can't be resolved with a return of the stolen items and a booting/demoting of the officer, the victim can always leave the faction. When things get stolen by a low-rank, it's usually an interfaction issue that cannot be resolved internally. There's no way to resolve it, because there aren't any threats you can point at the person who just stole a huge chunk of your fleet. You can't leave the faction to get away from the issue.
That's not a suggestion, that's currently what can happen. That's why this thread has been formed. If a faction is not careful, a 4th level member can access the faction module and set everything to personal at a station, no restrictions on what you can or cannot have set personal.
That's the issue, and we have this thread to help work out the kinks of the new system. If we can get the flaws and "unintended game-play" consequences out of the way we will have a better game in general.