Everyone's entitled to their own opinion, but I just don't understand this. Not only did MM (and LA for that matter) not spell it out for you....it completely chose not to acknowledge that at all. In fact, MM dodged it completely. To me, these aren't philosophical ideas the game had...these are plot holes turned into philosophical ideas by players with more imagination than the developers.
This is due to my own interpretation of a philosophy in-game: that which cause the player to give pause to his actions and consider the implications of his actions and how they affect the world around him, to act on those thoughts in-game, and to come away from it with a new way of thinking about things. These two games I've listed, Majora's Mask and Link's Awakening, have done that for me. While it was not spelled out to you, I was able to pick up on these two things while playing, and it caused me to stop and consider things from different perspectives and to act accordingly.
Honestly, that would have been awesome if Majora's Mask brought that question. Like maybe after the 2nd dungeon, Tatl would question their efforts when everything gets set back. And maybe, in the end, you would beat all the bosses again to free all 4 giants again before taking on Majora. But no. Instead, despite still be possessed by the masks, the giants are somehow immune to whole time travel thing. They are freed from the masks and yet the areas are still in peril. Why? Because the giant that is freed from the mask is still trapped in the mask and causing the problems.
Strictly plot-wise, yeah that's kinda a plot hole. Unless you subscribe to the theory of time traveler immunity, where the traveler and everything that travels with him are protected from any paradoxes that might happen. Also, that would be really freaking annoying if we were forced to beat each of the bosses before calling the giants and stopping the moon. From a gameplay perspective that would be redundant, and it might have deterred some players from ever finishing the game (something I think we can all agree would be a very bad thing).
I think the reason Tatl doesn't bring up the fact that your actions don't really matter is because she's focused on getting back to her brother. It does make for a simplistic way of looking at things, but it's consistent with her character. Besides, even if she doesn't we as players do. We start to wonder if it's even worth it to save that old lady from getting robbed because it's just going to keep happening. Whether it's even worth it to bring Kafei and Anju back together because it takes up the majority of your 3-day time limit and it's just going to be reset in the end. Whether it's even worth it to take on Goht and stop the winter because they're going to die and come back anyways. And even whether it's even worth it to stop the moon from falling because it's inevitable. Unless you have the strength of heart to push forward, free the giants, and stop it.
If that wasn't a huge enough plot hole, Nintendo dug themselves deeper in the end. The characters live a happy ending in each of their personal lives as a result of Link helping them...even though...Link didn't help them...because he went back in time. The Gorons should be dead. The Deku princess should be missing. Anju and Kafei's relationship should be over. The cuccos should still be small. The twins shouldn't have the new dance. The list goes on. What could have been interesting and though provoking story content is, instead, a plot hole. A huge one at that.
I am going to have to agree with you on this aspect, strictly plot-wise. What would have been better is if the ending only takes into account what you did during that 3-day cycle immediately before you beat the game. If you killed Goht and brought an end to the winter, then it shows the mountain in springtime. If not, it's a frozen wasteland and the Gorons are all frozen over. If you didn't kill Twinmold, Pamela's house would have been wrecked and invaded by the Gibdos, and they would have been killed. If you didn't go through the efforts of reuniting Anju and Kafei, there should be no wedding.
However, from a gameplay perspective that would have been inconsistent. If you went through the troubles of going through all the sidequests, then the ending should be a reflection of what the player accomplished. Since you did in fact save the four lands in previous time cycles, the game should show you what happens as a result of that (even though on reflection it doesn't really make much sense chronologically speaking).
Also, I'm still going to argue that the sidequests are thought-provoking, plot holes be damned. It still managed to cause me (and a number of other players as well) to think about my actions and the futility of it all.
L.A.'s is a minor plot hole but a huge disappointment in story. There was no regret. Link just awoke the Wind Fish and everyone died. Link didn't care. The windfish didn't care. This could have been a huge part of the story. Link having to struggle with the ominous warnings, perhaps confronting the owl and abandoning his destiny or Marin finding out and being a part of the big picture. But no. Link is told several times that everyone will die if he wakes the windfish. All Link has to do to keep an entire island alive is to simply...give up and stay on the island...which, when you think about it, is better than being lost at sea, doomed to be killed. But no. He keeps going, doesn't hesitate for a second, doesn't confide in anyone in this or even bring it up. And when all is said and done, he doesn't care that any of this happened. Who won in this? Everyone dies in an apocalypse and Link dies a slow painful death due to starvation and dehydration.
Again, I'm going to have to refer to my definition of an in-game philosophy, in that it requires to think about the implications of his actions and to act on these thoughts. These things you're mentioning, the struggle between giving up & living with Marin and awakening from this illusion of an island & erasing everybody else from existence in the process, are
intentional. The game makers wanted you to think that while playing. Is it better to give up your ambitions for the good of others, even if they are not real? Or is it better to cast aside illusions and face the reality of things, even if it causes things which you hold dear to fade away? Take the red pill or the blue pill?
You're arguing that it would have been better had Link simply given up. That's good and all, but what about him? He knows it's all fake and is reminded of it constantly. The islanders have no grasp of the concepts of time, place, of the existence of other lands besides their own, etc.; very fundamental aspects of reality that Link cannot help but pick up on. He would never be able to rid himself of these nagging thoughts because that is reality, and Koholint is not reality. Those people aren't really there, it's all an illusion caused by the Wind Fish, and all Link has to do is awaken him to get back to reality, to the things which truly are real; Zelda, Hyrule, etc. It's the classic struggle of the perfect illusion vs. cold hard reality: which would you rather prefer? In the end, though, Link chose to carry on through and strive to get back to reality instead of buying into the illusion, which I would argue takes a strong and heroic will to carry out.