I agree that it is an amazing JRPG (a model which more JRPGs should take notes from), though I don't really think fans don't so much "really appreciate" it as they grow (much with as the game grows) they learn to appreciate it's more subtle themes and messages. Much like how the Mother series is about growing up, as the player grows up and replays the game they learn to appreciate those things they never noticed before. I think that is part of it's enduring nature is THAT it changes, and how you view it changes with age. It's tale of love and loss, hope and despair, and coming of age is something anyone can appreciate, but as you experience some of it's themes in your life you grow to realize how much you can relate.
For example:
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Giygas' moral conflict between his duty to his people and his loyalty to George and (especially) Maria.
Lucas' tragic loss of his mother Hinawa and his brother Claus.
Ninten's absent father.
Porky (or Pokey to those who know him as that) having feelings of loneliness and truly missing Ness.
Also, Porky's obvious regrets with the past even if he tries to deny them himself.
[/spoiler]
There are a lot of things on one level or another people can relate to, and it's one of the many reasons this is also a valid argument as to why and how video games are indeed capable of being real art (though that's a debate for another thread :P).
edit: Weird, I'm not sure why it double posted, sorry all. :)