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I figure that Braig was one of the first that Xehanort connected to chronologically (because time travel is a bitch), and that would make Xigbar second right? But then again, Xemnas and AnsemSoD are LITERALLY Xehanort, so wtf do I know.
I didn't see that scene as Xemnas following orders, i saw that more as Xigbar going "You know what, screw this! Xemnas, you're strong, take care of Sora, I'm done. " More or less equals, but one of them was copping out.
Well, Xemnas does sit in Xigbar's old seat now so he's the new No. II, I figured more that he and Ansem SoD function now much more like Master Xehanort's top enforcers/Generals while Xigbar and Young MX (who interestingly sits in Larxene's throne) are more like Field Commanders.
I agree though that Xigbar wasn't issuing orders, he just let Xemnas take on Sora because he knows that Xemnas would be a harder challenge than himself.