That's exactly my point. Xemnas didn't let Xion into the Org., not really. She had a cloak and everything, but apparently Xemnas kept her on a short leash, so to speak. No column to sit on, no obvious missions, nothing. You'd think that if he found another Keyblade weilder like Roxas he'd use her as much as possible, but that's not the case. Also, if she can use the Keyblade, that means her true self could use one as well. There are only two girls we know of that could do that: Aqua and Kairi, but Kairi was not a true Keyblade weilder, so that kinda shifts toward Aqua. Now, there are only two other people who look like her in terms of skin color: Xehanort's Heartless and Diz's disguise. Diz's disguise was just that, a diguise, and shouldn't be taken too seriously. So that leaves Xehanort's Heartless. If Xion was a Nobody, she would've at least retained the same skin color as her true self, as evidenced by Nobodies in general. What I'm saying is, what if Xion is a Heartless? One just like Xehanort's Heartless, willingly joining the darkness and keeping her body and whatnot? We know that Kairi has no corresponding Heartless, so that leaves one person: Aqua. It explains why Aqua's armor is in the Room of Sleep, while Aqua herself is gone. It also explains her change in skin color, since there is no other person in KH with that skin tone. And lastly, it explains why Xemnas didn't use her very much. Maybe he didn't want the others knowing who she really was, or that he let a Heartless join the Org., or he might have not even trusted her completely, being Heartless and therefore having different motives than him and the other Org. members, thus the "short leash".