Actually, most of the time, Zelda IS fairly wise. The only exception is Minish Cap, in which she's a ditz.
Princess Zelda in LoZ hid the Triforce of Wisdom in places where Ganon couldn't reach it, and the Hero could. Zelda herself is probably the one who created all the traps and monsters inside the dungeons to stop people from entering, not Ganon. If Ganon had the Triforce of Wisdom, he would have had it himself, not with his minions. Ganon is only responsible for the monsters on the overworld, and protecting his own lair. In other words, magical monsters were probably just a common defense in Hyrule at that time.
Princess Zelda in AoL is unconscious for the whole game, so we have no clue if she's wise or not.
Princess Zelda in ALttP knew the way through the castle, and what Agahnim was planning. She also communicated useful tips to you telepathically.
Princess Zelda in OoT had prophetic dreams, disguised herself as Sheik, and actually guided you through the quest.
Princess Zelda in WW and PH was a clever pirate leader who often had ingenious ideas. How else would she have survived as a pirate and become their captain?
Princess Zelda in MC... okay, I'll give you that one. She's a total ditz.
But are you getting my point? Zelda is actually quite wise. She just doesn't have any power to back it up. You would be surprised how useless wisdom is without power or courage. Power is often needed to make use of wisdom. Courage is needed to even attempt to risk using wisdom. Without either, you're just clever, but too scared and weak to make a move.
I should know... I'm considered very wise, but I'm actually very helpless and dependent because I don't have the power or courage to make use of my wisdom on my own, either. Ironically, knowing this doesn't help me as much as you'd think.