For where I see it, Xemnas used the organization to collect hearts but not knowing that budding hearts were being born from themselves. Those close to Xemnas began to change into Xehanort (Xigbar and Saix). Xemnas wanted KH to become a god like bieng (think Aizen but more sexy). creating Xion, bring Roxas into their fold, Castle Oblivion, Namine, Sora ,the chambers, all peices to Xemnas and Xehanort's game of chess. But why want the contents of the Chamber of Castle Oblivion, why keep Aqua's armor and keyblade, use Roxas and Xion to collect hearts when Xemnas could have done it himself.
Simple, he wants them to believe that Roxas and Xion were special and collect hearts for them (in theory of course) so those who are not loyal to him would be no use to him and those loyal to him, well you saw in DDD. He sent the CO team away and even sent Axel to do his dirty work. Then again, Did Vexen, Zexion, and Lexaeus want to betray Xemnas, that's another story.
You know when alot of people say Xemnas is Terra and we should be sorry for him. Well, Xehanort is a monster and needs to be destoryed. Many lives he ruined, many worlds were harmed in the process. No pity from me, I want him dead.
That's my two cents and I know certain people will come for me. But I'm not worried.
But I might look into it more.