What does it mean when an FC aligns with a GC? Does the FC get some kind of bonus to the faction? Or does the FC fight together in GC battles? Reason I ask is that I want to know if I should pick the same GC as my FC did. Is there any reason to, or is it just window dressing?
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For the FC it allows them to buy the skill boosters that get applied to all members of the FC (like +5%xp, reduced durabilty charges, etc). So the FC wants to align with something.
As of right now, it doesn't matter who you align with.
As far as your personal GC, it doesn't matter if your the same as your FC or not. There is no bonus as far as I am aware of.
In the future, when the Battlefronts come out, your GC alignment will determine your PvP faction. It's unclear to me right now if personal GC or FC GC will get used to determine where you line up though.
You can switch your personal GC, so not sure that it really matters even in the case of PVP