Upon reading the title of this thread, I immediately thought of Ganondorf's appearance in
The Wind Waker. I will point out that as the bad guy; there will always an element of cockiness present which kind of makes the majority of the series' antagonists rather dull-witted and oblivious to an extent. I just feel that when that particular mindset is least present, whatever intelligence that exists can actually be expressed rather than overridden. Ganondorf in
The Wind Waker—unlike Ganondorf in
Twilight Princess—has already experienced a technical defeat once before in
Ocarina of Time therefore a lot considerations have been made in his schemes on the Great Sea. I'm not sure if the rate of time-flow was equivalent to how it is in Hyrule to where he was sealed, but he did have some time to reflect upon errors.
Upon his return, I sense his actions were on impulse. However, when the rains came from the heavens endured as such an attempt to imprison him beneath the waves, I think that was another smack in the face to him. Another failure on his part to grind away at his overconfidence. Just by the way that he managed to escape to the Forsaken Fortress by using a dark portal, hints intellect. The King of Red Lions didn't even know how Ganondorf fled nor did he know it was possible.
Ganondorf also used reverse psychology in
The Wind Waker on a certain level. Just the fact that he knew if someone aspired to confront him, that person would have to unknowingly break the seal that by which the Master Sword bound him. Also by killing off the sages who offered up prayers to keep its power alive was a significant sign of premeditation of the entire scheme. Upon Link's second meeting with Ganondorf atop the Forsaken Fortress, had not Komali and Quill come to his aid, Ganon would have been at full power with no one to stop him.
And, if you really think about it, Ganondorf would only hope that there would be a chosen one just so that he could reform the Triforce of Courage and retrieve it. For being the fool he was in
Ocarina of Time, Ganondorf reformed the Triforce
before any final battle had time to take place. As if Puppet Ganon were a way to rub that in before hand, to wear Link out so that his defenses were down.
Yes, other than some miscalculations on his part (like the distance of the Triforce from his hand
), I do have to say Ganondorf as seen in
The Wind Waker was easily the most intelligent antagonist in the series [in my
nion:]. Poor judgment and impulse isn't necessarily synonymous to stupidity, but that might have still been his fatal flaw. Inevitably so.