I love nothing more than a side quest in a game but I would agree that I played most of my way through the game without a guide then looked in a guide I owned but had never yet used. It turns out I'd missed so much.
Example the little waterfall puzzle in the Sochen Cave Palace was a bit unreal as there was very little clues as to it's existence. The route was so specific and abstract, I highly doubt many people would have chanced upon it. Also, how obvious is it that the key to the Hell Wyrm is in Windmill number ten on the Cerobi Steppe??

Same with the Zodiac Spear, you see a chest, the automatic reflex is opening it, especially when the one outside Old Dalan's house actually appeared in a cutscene, drawing the player's attention to it.
Without previous knowledge there is no way that a player can possibly know there are four specific treasures they cannot touch, it's absurd.

So in effect Im in agreement with the OP, many of the side quests specifically require background knowledge or there is no hope in hell of ever completing them.