artistic freedom. plus, X6's sealing is not the one Ciel finds him in. the X6 sealing is the first seal, and the one "shown" in Z1 was the Telos interpreted second seal. remember, in the original seal he was to be asleep for 102 years, to "remove a component". the second seal was supposed to be permanent. as also shown in RTRZ, where Zero's disembodied voice tells Ciel outside of the room to "leave him alone", and questions why she wishes to awaken him Telos itself asserted that he was basically taking himself out of the way.
also, its not jst omega that makes 3 so great, its the story, gameplay, weapons, abilities, and the much cleaner artwork the cut scenes and mugshots are made from, in comparison to 1 & 2. the recoil rod was brilliant, and its ex skills were real good. the story was finally at a climax, and just so potent. explaining almost everything that was needed to know. and the characters were really well played out this time around.
this time around, Harpuia really made me think of the mental aspect of X he is based from. (X's sharpness and wisdom)
and the music was incredible, reflecting the moods really well. Omea is the LASt factor in it all. just a byproduct of the story.