My biggest complaint with the storyline as it is is obviously the ending. I feel we were semi-robbed of a true ending. In my opinion, it's bogus from a storytelling perspective for the finale not to revolve around saving the Matoran Universe and the characters within it. "The three that must be one" and all that is a very cool idea, but wasn't built up over enough years for us to really care about it. In addition, no one cares about Gresh, or Gelu, or any of the Bara Magna characters, so a finale revolving around them and Mata Nui is dumb. Instead what I would do is build up the "three that must be one" thing a little bit better over the years and have us understand eventually that this is Mata Nui's purpose, but have it be that to fulfill that purpose, he must regain control of the robot. No Makuta/Mata Nui rock-em sock-em. Instead what we needed was a final battle with the Nuva, Mahri, Hagah, Dark Hunters, Matoran, Turaga, and all of the heroes and characters we love uniting for one insane final battle against Makuta and the forces of evil. Reign of shadows should've been the focus, or at least split 50/50 with Mata Nui's quest for his origin. He still goes to Bara Magna and Bota Magna maybe, but that is a side plot to the characters we love saving their universe. Nobody liked watching Metru Nui and all the locations we'd come to love be destroyed in favor of Spherus Magna. A lot of characters got shortchanged in the ending, in particular Takanuva. I would have Takanuva be CENTRAL to defeating Makuta, and thus have his role as a Toa of Darkness/Light and his "destiny" be revealed.