Well in next gen, Mephiles showed Shadow his future; and in the future Shadow was taken down and put in suspended animation again by OMEGA.
My question is, if this is a "Real" future and since time started over, couldn't that happen? with time starting over that = Shadow getting no warning, and wouldn't that make that future cannon? O.o

Well, when when Mephiles shows Shadow his future, he says that the people used the destruction from Iblis as an excuse to hunt him down. They always thought of him as a threat because of all of his power, though this gave them the perfect opportunity to blame it on him and stop him for good. Since time was reset and Iblis doesn't exist, there won't be anything for Shadow to be blamed on, so they wouldn't really have a reason to hunt him down, making that future unlikely.
Even so, if something else tragic happens then they could do just as they were going to do for the other incident and blame it on him, ect.

I'm not sure, but if Omega was the one to seal him in suspended animation in the future, wouldn't he be told to do so by the humans? If there's no reason for him to attack Shadow since time was reset, then I don't think they'd order him to do it. I'm confused about that part though, because Mephiles says to Omega that even though he's controlled by humanity, what he does to Shadow is his own choice. That's kind of saying that even without the destruction from Iblis, Omega could still turn on him. The thing is, I'm not sure if he's persuaded by humanity or not which causes him to make that choice.

Wowz0rz, that was hard to type. I know what I'm trying to say in my brain, though it's hard to tell other people those thoughts and actually have them make sense. x3