Fair point. I do find myself wondering if the events of the Crystal Tower are going to tie into the MSQ's somehow or if it's going to continue to be a side story that's disconnected from everything else. I suppose it may be as simple as a slight dialogue change with Nero based on whether or not it's been completed. Such as how Alisae's dialogue changed depending on whether or not the player in question had completed the Coil storyline.
At any rate the next Live Letter is due on 25th November so we won't have too long to wait until we have more information to discuss.
