In the game Four Swords Adventures, Vaati as a character is so USELESS. He's in his eyeball form, he says absolutely nothing to you when your party finds him, and he easily gets his ass kicked.
I know the main boss of the game is Ganon (and it's a party game generally speaking), but I feel like his character should've had more weight to the story especially after Zelda says that the palace in THE SKY is falling because Vaati isn't around to keep it up anymore.
He's THAT POWERFULL??!! AND THEY DID NOTHING WITH IT!?!?!?
So what if Vaati lived up to his powers and was a serious villain to contend with? This was the guy who was fascinated by evil Hylians and who spent a while trapped in the sword after Minish Cap (if you wanna include that game).
Wouldn't he be at least a little insane from all of that isolation? How would he react to fighting against the same hero from before? Would it be personal?
In my opinion, it's totally personal. There's no way he wouldn't get revenge on Link and Zelda after they sealed him in that sword and almost drove him insane. I feel like Vaati is a smart enough character to realize that he was starting to lose it, too. So that's even worse for him. He got combo-ed!
Revenge though? What kind? Ending the both of them would be efficient and ultimately the best for his evil plans once he's freed from the sword. But he was stuck in there (for the most part) FOR YEARS. The simplicity in that is too convenient for them.
Making them suffer for a long long long time is right up his alley! There's no better way of doing that than stealing Zelda away from the people and the land she cares for and making Link fight with himself every time he tries to do anything.
Zelda staying the clouds with him symbolizes his insanity, since she would absolutely hate it up there, while Link being split into different extremes of himself is proof of concept. If there's anyone that can stop Link, it would be himself right?
He does this and more in the fic I'm writing! Feel free to check it out!