It had a good solid story that wasn't contrite or convoluted as shit. The evil organization / government Shinra is a overly direct jab at the oil industry. The characters are all well rounded if lacking in back story and had not one but 2 twists you never see coming.
The death of Aeris and the fact the Cloud wasn't who he thought he was (granted the memories portion of the story was horribly boring). In optional cut-scenes we learn the source of Vincent's torment, the creation of Sephiroth, and Cloud's persona's origin in the death of Zack.
The side quests we part of the story not just random side shit, and all of the ultimate gear was obtained/contained within the story's structure. Tifa's was in here piano (required playing the song she did as a child, Vincent's was with his wife - also the mother of Sephiroth, Cloud's was taken from ultimate weapon (one of the earth guardians).
The best part is every single character had a believable reason for doing what they we're doing.
It had the usual hippie peace loving undertone but wasn't about whinny feminine teenagers; It came right out and made the point that sometimes peace can only be won not negotiated. Both Barrett and Cid we're old gruff guys. Aeris was a flower child, Cloud was a solder in the army.
And all the materia management for the magic system resonated with that part of the human mind that still compels you to capture all the pokemon in the world.
It is a jrpg but easily one of the best, and I'll hold it up as one of the best uses of story telling through gameplay.
Oh, last but not least inbred Chocobo breeding FTW.