[AndreaDraco83]

I think that a difference between the three aspects can be extremely useful. If the story, but I'll say the storytelling, it's what captivate the attention of the player, the fil rouge that, in the end, keep him close and interested, the very core of any narrative-oriented medium, and if the exploration is what gives the player the feeling of immersion (I'm not looking at the room, 'cause I'm in the room, I can visit it thoroughly), the puzzles are the device by which the player inter-act with the environment, finally realizing, giving substance to the feeling of immersion.

For example, a dialogue puzzle fulfill the need of a character interaction, whilst an environment puzzle fulfill the need of material manipulation and so on.

So, if their final purpose is to substantiate the player immersion/presence in the game, when they're poorly designed they ruin the suspension of disbelief eventually spoiling the final experience of the game (but it can be a movie or a book: also in these media there are instances that serve for the immersion/presence of the viewer/reader).