Exoria/WMG

Valent is looking for the triforce of Courage's birthmark
It has been mentioned that Valent is capturing civilians without harming them. They are looking for the one who bears the Triforce of Courage so that they can do... something with them. Seeing as how this has occurred before, in Twilight Princess, it's not so far fetched that this is happening now.

Link is the heir to the Valentine Throne
This one is mentioned in the reviews, but this troper agrees with it. Hyrule is Blue and led by the traditional holder of the Triforce of Wisdom, and Gerudo is Red and led by the traditional holder of the Triforce of Power. Valent is green, but it's main royal family is thought to have been killed in the Valentine Revolution. However, this was never confirmed, so it's quite possible that King Adam III and Queen Eileen fled off to Hyrule and had a child, and then were killed or died of some other cause. This child was Link, the traditional holder of the Triforce of Courage and rightful heir to the Valentine throne.
 * This would fit well with Link's tendency to be an orphan hero

The plot will somehow be Hijacked By Ganon
Is anyone else suspicious of the fact that he's an ally instead of evil in any way?
 * Honestly, I wouldn't be surprised if we were treated to a MGS-esque twist were it's revealed Ganondorf was behind everything all along. Well, to be frank, I would be surprised if the author managed to explain it in a way that made sense.
 * Or the Original Ganondorf is behind it all the Generalisimo is just a male gerudo named after him.
 * As of Chapter 14, this may be happening.