I've thought about this too, and right now it seems to me that it all comes down to the difference between fanfiction and actual published stories.
It's important to consider that, in the 'real world', works are judged differently than a fanfiction would, posted in an online community. They are judged not only by the quality of their writing, but also by their meaning, and their effect on people. Why, for example, is War and Peace considered great? Whether or not you think that the characters could have been written better, the description done better, etc.,it's valuable because it gives the reader something more than a pretty mental reel of scenes. It gives them a vivid glimpse of a historical event, and of society, of the beauties and tragedies of life, and contains serious, thought-provoking themes that, though they might not be encoded in a writing style that the reader finds pleasing, they are written in such a way that they will reveal themselves if the reader spends some time to think about them. Such a story is like a treasure chest. The case might not be anything out of this world, but if you can open it, then you'll find the real value of the story -- a common element that everyone can appreciate. And once you've found that, you'll realize that it transcends the possible flaws of the actual writing. And then you won't spend time thinking about how this character's emotions should have been 'shown, not told', or how that scene could have been more elegantly described. Because you'll realize that, despite all those things, the writer still got their point across, and it was a valuable point indeed.
Readers who are able to find this 'hidden' meaning will value the story for something beyond the quality of its text, and if this happens to a large enough segment of society, the work will become famous, and maybe even great. And so, a writer may rise to the top because he/she writes meaningful, relevant things, and has written them in such a way that readers can access them.
I'm not saying that anyone who doesn't like a 'great' work has somehow missed its point or hasn't thought about it enough. In some cases, the style of writing is enough to turn me away from a famous story, in which case I'll simply set it aside and say that I didn't get the same impression as its fans did. That doesn't mean that the book is meaningless; I just found that my complaints about the writing overwhelmed any pleasure I attained from trying to read deeper into the text. Different people definitely have different tastes, but by no means is your opinion invalid if, say, you see a paragraph that the author could have done better, or you don't find the meaning of the story worth the strain of extracting it from average, or even low-quality writing. It's happened to me, too. I just make an example of writers I like, and write with the style that's best for me and my story.
Now, on a fanfiction community, stories are judged differently than in the real publishing world. Fics don't usually cast such large reverberations on the fanfiction society (at least, not that I know of) because they're written in a different way. I don't think it's likely that a fanfiction would be praised for its 'beautiful portrayal of Kanto society' or for 'launching a revival of the spirit of pokemon training', because really, those things can mean whatever you want them to mean. Every reader is going to have their own interpretation, their own two cents, and even if someone did want to become the Tolstoy of Pokemon fanfiction, there would be at least one reader who would want to do things their own way, so in the end it wouldn't work out.
That's why fics are valued for their stylistic aspects, and for the creativity the writer displays when building their own version of the Pokemon world. Judgment is placed especially on description and imagery, and other mechanics of storytelling, because those are your only tools to engage your reader in your version of the Pokemon world. After all, Pokemon isn't something we all share as human beings, and every fic writer puts their own spin on it. No matter how mind-blowing a fic may be, someone else will always find a way to do something different and come up with their own reinvention. And it would be perfectly valid of them to do so.
So, in short, I believe liking a story is a matter of personal taste, and even when it comes to famous works, you have the right to judge according to mechanics. But sometimes, a story's value can transcend the style of writing, in which case it's all a matter of whether you tried to find it, or whether it's important to you or not.
