While this is rather interesting, one thing bugs me.
Could Nintendo have planned the OoT story (split timeline) before the N64?
I don't believe that. If they didn't, they must have either made all the pre-OoT games fit into one timeline, or two timelines. Personally, I find the former more likely. If the latter is the case... Well, then the timeline is screwed, because the Old/Young ending from OoT was a forced fit.
The entire child continuation of the story is ridiculous, seeing as Link could, at any time after becomming adult, have gone back and warned Zelda. It makes everything you do as adult completely meaningless. That's ridiculous. Of course, this prevents MM from happening at all. Either way, I find the child timeline to be "fake", as its origin couldn't really have ever happened.