I guess i should have stated that better then.
I'll juse majoras mask as an example, as the game has one of the best atmospheres of any game I've ever played, likewise, I was playing through the game all last week, so that its still fresh on the brain. (I get tales today though! w00t!)
The 3 day time limit is made obvious throughout the whole game, earlier during the 3 days, people just ignore the moon hanging in the sky, the music in town is cheerful and happy, people just carry on with their normal lives. However, as time goes on, the town music changes to become a little bit more frantic, and people start worrying about the moon thats about to hit them, Theres an argument in the mayors office about making people evacuate the town, certain people realize that nothing good is going to happen.
Then, on the night of the final day, the town is basicly barren except for a few select people, they're incredibly worried about the moon thats about to fall straight down on the town, the music is incredibly depressing and omninous, and it seems as though all has failed. Of course, the issue is that all *HAS* failed if you haven't beat the game yet, so you have no choice but to repeat time, and hope to get things right next time.
I didn't mind having to "talk to everyone over again" because I rarely do so, you have to choose what your doing those 3 days and stick to it, you can't save everyone. I liked that, kept the atmosphere higher, if you wanted to help someone, you had the chance, but not everyone can be helped. Sure, the fact that you had to go and repeat a boss battle to save the land every single 3 days was a little taxing, but luckily the warp makes it much more manageable, and i really enjoyed all the boss fights with the exception of the damn fish.
The people in majoras mask change what they say depending on what day it is, they have certain actions depending on certain times, and were generally just far more *alive* than they were in any other zelda game. The reason for this is because of the forced time system the game had, it allowed the atmosphere of the game to keep getting thicker and thicker as the crisis was about to befall the town. Windwaker failed to have that atmosphere, so did OOT, because nothing seemed that rushed, that important, sure, ganon may rule the world. but you can happily go and wait another few years before you have to fix it. In Majoras Mask, if you sat around and don't get things done, the world is doomed. How do you know its doomed? You can see the signs all around you, the music, the people, the gigantic moon staring down at you that stretches all the way across the horizon. It slowly gets closer, closer.... and then if you don't reset everything, you see it hit the town, and wipe out everyone.
Even in Pikmin, the 30 day limit (far more than enough in my mind, i tend to beat the game before day 20) was just a slight sense of urgency, however, the 15 minute daily limit forced you to worry about what you can possibly do with your pikmin and get done before the time is gone. When its approaching night-time, right before the 10 second counter shows up, you start getting worried about getting all of your pikmin back to the ship in time. Part of the reason your so worried about the little guys is because of the cuteness miyamoto shoved into them, and you don't want to lose a single one. If there was no time limit, you wouldn't have to do the mad dash back to the onions at the end of every day, and your emotional attachment to the little devils wouldn't be nearly as strong.
Having control over every single element of a game tends to remove some of the atmosphere, In Most RPG's, despite everything you do, you still end up failing the mission before you accomplish it, however, the sense of urgency and demise just isn't there because you know that, regardless of the meteor thats about to hit the planet, or the fact that theres some sort of god on the loose that wants to destroy everything... you have as long as you want to go and catch butterflies to try and get that final weapon. Stuff like that, while keeping the gameplay better, does completely destroy the *omg were all gonna die* atmosphere, hell, most people in the game won't even notice that theres some gigantic being right outside their hometown, and just carry on like nothing has happened.