In most RPGs, it doesn't matter what's more important - you can take all the time you want to care about minor quests and errands, as the main story only continues when you actively trigger certain key events.
While I value the freedom connected to this design, I think it could be an interesting dilemma to let the player choose between quests, only some of which can be completed before something else happens. Imagine there are five quests in a village, but you can only complete three before the entire village is flooded or raided or evacuated or whatever. You'd really have to decide what you consider most important, possibly touching moral issues when you choose who can be saved or helped. Of course, the game should let the player know that it's not possible to solve/complete everything because of the circumstances.
This would add a lot of replay value, however, some players will probably hate the concept because it would practically force them to play the game more than once in order to see everything there is to see.
I can't say I like that idea, Lurker, sorry.
If the player knows something bad will happen to the town, number one quest usually becomes to STOP it. If that's not possible, I for one would get very frustrated.
If the player doesn't know and starts working through quests in random order then finds he's suddenly out of time with no warning... That's frustrating, too.
I don't mind time limit quests, though, like in the original DD where you have X days to deliver a message or something like that. That way it's up to the player if they succeed or fail.
