- Note: I'm just tossing up some initial ideas here for now. I'll probably come back to edit and flesh-out this post at a later time. Also, there may be potential spoilers so read at your own risk.
While it may not have been the best implantation of the concept, Majora's Mask (MM) was the first game I ever played that made me contemplate the idea that I couldn't save everyone. At least, not without the aid time travel.
Even when you completed a dungeon or a side-quest, the fruits of your labor (not including the equipment and masks you received) only lasted for the remainder of the moon's countdown. After you completed all of the major dungeons, you could go back to them again to skip ahead to the boss battle, and fix that part of the world once more - but all of the characters had their own schedules. Even if you knew exactly when and where you had to be to finish a side-quest, I don't think it was possible to finish *everything* in the three-day cycle. I'm pretty sure there were cases where you couldn't be two places at once.
This is a big factor as to why I'm so fond of this game. Up until this point, most if not all of the games I played followed a very linear path. You could ideally solve everyone's problems before taking on the last boss and finishing the game in one big happy ending. In MM time travel enabled you to help everyone, but not in the same way. Or, more importantly, not with the same "satisfaction" as before.
In older games, you solved a puzzle, earned an item, and an NPC would just repeat a thank you message. In MM, you solved a puzzle, earned a mask or other item, but the resolution for that character's plight wasn't really permanent. The smile on their face would only last until their world was ultimately destroyed, or you undid your own work by going back in time. If you ever want to see them happy, you have to do the work all over again. No new item or mask as your reward, just the satisfaction of knowing you helped someone. For me, this made certain quests more precious in that they felt more "finite." For example, reuniting the engaged couple was arguably the most difficult, time-consuming side quest in the game - and one you could botch right at the end if you messed up. The first time I completed it, I actually waited out the impending apocalypse to see if the NPCs would stay or flee the town. I had become invested in them. I cared about their problems. It wasn't just about completing all of the quests and getting all of the masks - I wanted to know what was going to happen to these characters depending on my actions.
Now mind you, the game didn't have a perfect system. Time travel in any fiction suffers from loop-holes and paradoxes, and there was a way to get "the best ending" by collecting all of the masks and seeing everyone's individual "happy ending" during the credits. It didn't make sense that you helped someone once, undid your work via time travel, and then when you beat the game somehow your first efforts carry over. They tried to write it off/into the fiction with the masks, so maybe that's an issue of suspending one's disbelief.
My point is, MM suddenly made me really care about helping the characters and struggle with my desire to try and save everyone. In then end it was satisfied, but the fact that I questioned it throughout my first play-through meant something to me. I had to actually doubt what I thought were the set rules and limits of the genre: Isn't the hero supposed to fix everything for everyone? Isn't failure to do so always my fault as the player, not the limits of the protagonist in this universe?
Now that I'm older, I frequently have to face the fact that I cannot save everyone. I cannot help every homeless person, every starving child, and every oppressed minority. I will never be satisfied, no matter how much humanitarian work I commit to. But I can help *some* people. I can enjoy the happiness I bring to other people's lives, no matter how brief or fleeting. I'm not saying that MM was the most significant factor in how I deal with these issues, but it did get me started in thinking about some core philosophical ideas. Like any creative work, I often attribute it's value to how it makes me think. That's a big reason why MM had a lasting, positive impact on me.