Well I just read your first thread about your theory. You definitely thought about it and seemed to have a pretty good tangent going there. I don't know if you can consider "Phantom" and "Shadow" one in the same, though they are similar. Now, if your theory is indeed correct though, and the next title includes "Water", I could see one possible storyline. The Hyrule of the past as WW described is buried in the oceans, but the game didn't delve into the sunken city to my liking. What if they combined the basic concept of another deminsion like the Twilight one, but with the Sunken Hyrule, where link travels back and forth between the present islands, and the sunken city, possibly running amongst the Hylian spirits. Which brings me to a point by itself:
For the two different timelines of the Zelda universe, there's a twilight dimension for the Child timeline, but is there one for the Adult timeline? If so this could play out VERY well with your theory (if it is true).
Also, just because it's in the Adult timeline (timeline of the great flood, etc.) doesn't mean it has to be a sequel to WW/PH per se, it could feature a new Link to explore even farther in the future of the Zelda series, atleast in that timeline.

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...faith in hope...