A mission storyline, whether put in place by exact quests or by simply having the NPCs and certain plot locations necessary to progress several different ones, is needed, but it doesn't need to be as urgent as an actual "mission". General plot connectablity is just as viable, and does not limit the city's use to just a small set of quest lines. Phasing it the zones into oblivion as with Cataclysm's Vash'jr and Mt. Hyjal, inversely, tends to leave only a shoddy mess of a half-assed plot progression. If something showing the effects of player actions is implemented, it would probably do best to show not only your actions, but most in general -- such as a town under attacks from rebels via stealth and explosives. And you're in the thick of it, without clear belief in either side's doings.
WoW examples aside, I agree that being locked into places such as to create the feeling of really being lost in a jungle or unable to escape from a city can be great. However, there's a lot that can still be done with less urgency in these zones. NPC relationships, discoveries, and more gradual plot developments will each carry a unique spin just from being there, as long as they are part of a larger plot. That plot does not need to show itself as obviously as through actual sabotage.