It might help if quests were related to each other in some way. Basicaly, overlapping in terms of storyline that shows some commonalities across various quests in certain parts of the story. So, an example might be if a PC were to descend from a level to another to search for something as part of a main quest, between those two points, there might be something else of another quest that has to be initiated, something like a side quest, but which does not need to be completed. This allows an opening of other story alternatives rather than merely linear advancement. Just an idea.