Does your game world exist outside quests?

Items
"Find a penny, pick it up, then the next day have good luck."  Or in the MMO universe, "Find a quest item, you can't pick it up, maybe next time around you'll have better luck because you'll have gotten the quest first, noob."

"Does this thing exist?"  In the real world this leads to all manner of philosophical musing, mo less than most of it utterly useless.  In the virtual world the answer is complex.  An item may exist, but what the existence is may change.  Without the relevant quest it may be in a mob's inventory, waiting to appear.  Or it may be an object on the ground, with appearance and may even physical interaction with the world, yet it cannot be picked up.  In some very rare cases the item is a quest item and it will exist with or without the quest, but the quest is merely piggy-backing off non-quest items, such as turning in gold or trade materials for reputation.

If a quest requires an item to be picked up, what should the item be without the quest?  The developers could leave the items out, waiting to be picked up, regardless of whether the players has the quest.  Then it becomes an inventory issue.  Are players going to fill up bags with currently-useless junk?  Can they destroy the quest items, rendering them incapable of completing them later?  Will quest items take up no capacity?  That can end up looking strange if the quest item is more than pieces of lint, which is itself rather strange.

If the quest item does not exist yet or cannot be interacted with without the quest, then the world itself is altered by the presence of the quest.  At times this may have an explanation, such as if you previously lacked the magnifying glass needed to see the pieces of lint.  At other times it instead appears that your character is magically blind or utterly incapable of expressing any interest or interacting with particular items in the world, until someone asks about them, and then no longer once the questions end.

This latter method is most glaring when the item has little reason to have not been there before.  While the quest may explain that the villain fled and left something behind, it often does not.  Even worse, you may go through an area and kill the villain, but he leaves nothing behind without the quest.  Seemingly immobile items, such as tools in an abandoned factory, may or may not be there depending on the quest, suggesting that Quest Gnomes are sneaking into abandoned factories to leave tools, which means that they should properly be called not-so-abandoned factories.

Phasing
In WoW we saw the rise of phasing.  While it is a neat idea, and makes sense, that the world would change in response to player actions, that is not actually what happens.  It doesn't matter if you kill a billion mooks and bosses, your side will never advance.  Instead, they will advance after you complete the quest that calls for you to kill ten mooks and maybe one boss, though those only count if done during the quest, and killing extra has no impact.  The world is nothing without the quests.

Story
*muttering to myself* "What's going on here?"
Nearby exclamation point guy: "Let me tell you, brave adventurer!"
Me: "I'd like to figure it out for myself."
NEPG: "HA!  You can't."

In a mystery novel you may be able to piece things together.  You might figure out the villain before the big reveal.  You might anticipate the villain's next move.  The facts may be there to figure things out, but lack the narrative structure and analysis needed for less-brilliant readers to figure things out.  Or there may be some facts missing, so that competing theories cannot be eliminated yet.  Despite the incomplete story, it is still there and you can create a narrative, perhaps incomplete or even wrong, but based on something.

Quests tend to hijack this process.  The world is presented, but it is nearly a blank slate.  It is merely there.  You cannot ask it anything, you cannot investigate.  There is nothing more to learn.  There is certainly not enough to form any sort of explanation for why it got to be as it is.  Instead there are quests.  They explain why it is how it is and how to change it to what it will be (though with likely no mention of how you want it to be).

It is like playing Clue, but rather than seeing that the victim is the maid, with a bloody candlestick nearby, and a trail leading down to the wine cellar, you instead are told that the maid has died and you are sent to investigate the body, leading to a quest in which you look for nearby blunt weapons, which are of course sparkling ever so slightly, and then you're prompted to follow the trail of blood, which is also sparkling and you may not have noticed until someone nearby who is apparently paralyzed in a standing state or is a faceless voice in your head prompted you to follow it.  Then in the basement you find the butler with a gun and a dozen armed minions, yelling in large red text about how he'll kill you for interfering, while the previously-mentioned paralyzed man or faceless voice do nothing at all.