I think that he could be the final boss, but personaly I think it will be someone/something that we never saw yet. I could be wrong, and someone might give me a million reasons why I am, but I just think that is how Nomura works. He always shocks us and puts twists in the game that we wouldnt think of, no matter how close our theorys are. I could see the DS and MX being bosses for two scenarios though, but I just have a feeling there will be something higher up they have to deal with in the end.
Also, I dont know if this has already been thought of or said that it will not happen, but does anyone think that once your done all three scenarios, it might open up one more where they go and deal with the last boss or last part of the game? Maybe the three scenarios are just leading up to the ending, but your not actualy done the game when you complete all 3, you've just led up to the last boss or something. Just a thought, nothing serious.
Also, I dont know if this has already been thought of or said that it will not happen, but does anyone think that once your done all three scenarios, it might open up one more where they go and deal with the last boss or last part of the game? Maybe the three scenarios are just leading up to the ending, but your not actualy done the game when you complete all 3, you've just led up to the last boss or something. Just a thought, nothing serious.