I think Nomura said in an interview that he had always envisioned a girl being the reason for Roxas' departure from the Organization, but had never put much consideration into it before because Roxas' escape was off screen (Until 358/2 Days was released) and Xion was not an official character (At the time). And Xion not appearing in Roxas' awakening is probably due to the same reason we never see Naminé's drawing of Roxas, Xion and Axel together. Because Xion was a memory based being, when she died all evidence of her existence faded away, except for I guess the consciousness that she claims she will have inside of Sora/Roxas.