Seeing as the legend is named after her, I hardly see that as qualifying for her to be placed into the role of a minor character. Even though you control the character of Link, it's about her.
I agree with you at least in part in most cases, but there are exceptions. Zelda was largely irrelevant in Twilight Princess, for example. Saving her at the end wasn't even part of your goal; the raid on Hyrule Castle was about stopping Ganondorf.
As for Zelda and the Triforce of Wisdom, you need to keep all the definitions in mind. Off of WordNet:
▸ noun: the trait of utilizing knowledge and experience with common sense and insight
▸ noun: the quality of being prudent and sensible
▸ noun: ability to apply knowledge or experience or understanding or common sense and insight
▸ noun: accumulated knowledge or erudition or enlightenment
#1 and #3 is basically good judgment. Using the knowledge and experience you have and making good decisions with it. You can argue that Zelda's made some bad decisions, but a number of those cases are still her acting to the best of her ability, and she has in numerous games developed some impressive plots against Ganondorf and the evils of Hyrule. #2 is a trait that fits Zelda well. She's not stupid. She's a sensible person. Sensible people are not immune to making mistakes. And #4 leads into my main point...
Zelda is a Sage in Ocarina of Time, carries a powerful and magical bloodline, and is the ruler of her country in numerous other games. She has knowledge; she knows things. She also has insight, either in the form of good judgment, advanced knowledge about magic and other cultures and artifacts, or just a supernatural awareness in her ability to communicate with people telepathically, sense evil with premonition or intuition, and whatnot.
No matter what game you apply it to, the term "wisdom" describes Zelda very well. The term is not as clear-cut as "courage" and "power" are.