the only issue I have with "puzzle" in this game is the button hunt.
anyway, your primary example of bad puzzle isn't really just a puzzle though, it's about a quest item essential to the story, which is quite common in RPG. oftentime in RPG, you need certain key item to move the plot along, and those items are mostly all over the place except for the particular place you'll use it.
D:OS is RPG, Portal isn't.
the pure, straightforward puzzle area in D:OS would be underground passage and Bellegar's Maze and the like.
