I still argue that LA has a better narrative. It's more akin to Metroid in that it doesn't need consistent dialogue. Plus, the owl makes a good ominous character there. Owl statues solidify it further.
And canon is definitely important if you want anyone to take your game's story seriously. That timeline is one of the worst things done to the Zelda series and I'll be damned if the upcoming Zelda games are devoted to tying that catastrophe together with them.
I like blaming MM's flaws on shorter dev time.
For the record, I don't consider any Zelda a masterpiece. Great games, but they're no Shakespeare among the gaming world.
Shakespeare is only great because of how it influenced society and Zelda is one of the most influential video games ever. But not all masterpieces are made that way. Why I view MM as a masterpiece is they way they go about telling the story and that story are the stories of everyone you meet.
Nobody plays Zelda for the lore. It's pretty craptastic. Ocarina at least bothered to expand on the little bit of lore there was. MM didn't care for it at all. Zelda's puzzles, dungeons, and world are its core.
Best way to explain it is by expanding your horizons. For every game like Xenogears, there's a plethora of CoD's and Maddens, but the struggle is completely worth it.