I believe the biggest reason for implementing this is due to the fact that the guilds with the highest amount of alliance take control of certain outposts.
We all know that there are huge uber guilds out there that have millions of faction. With degradation in effect, this ensures that if that guild for some reason goes to crap, they aren't going to keep those millions of faction forever, and thus have a dead guild with outpost control. Since it's a % the higher your faction, the more you lose. Thus the bigger guys have to work harder to keep their spots.
Livingston
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