To answer the "can a MMO have a story like this question,"

Yes, Final Fantasy XI had an amazing amazing story that was laid out well. The only problem was that the game was so brutal when I played (the early days until roughly around 07) that many did not see the whole thing to fruition. Promathia for example had probably one of the best stories ever done in a MMO. Hell, it was so good it would almost work as a stand-alone. The reveals were slow and ambiguous and some questions were left to our imagination. Again, since it was so bloody hard when it was first released many did not get to experience it.

Also, Rinoa is Ultimecia has been officially nixed by Word of God FYI.