I've personally read some excellent fanfiction - even a few examples that were better than the original. Though of course there will be lots of bad fanfiction, since it is being written by inexperienced writers and not professionally edited. Filler anime often has a difference in tone from the main series; it's difficult to tell if people are objecting to that difference in tone rather than any actual difference in quality. But filler episodes are constrained to be unrelated to the main plot of the series since they have to happen in a gap between pieces of the main plot. This requirement makes it difficult to make anything that will seem compelling to the viewer; it has to be more or less episodic, which can make it seem pointless to viewers.

For fiction in general, I would say you get a high quality story like this:

- The story has an overall theme or premise that unifies it and gives it meaning.

- The worldbuilding is internally consistent and expresses the theme.

- In parallel to the theme development arc, there must be one or more character development arcs. Character emotion is key to a meaningful story.

- There must be both an internal conflict and an external conflict, because any story with only one of these feels flat and shallow.

- The viewpoint character should be involved in the main decision-making and action-taking of the story, not just a passenger or pushed along repeatedly by external events.

- No cop-out endings. No deus-ex-machina, no it was all a dream, no ambiguous mess left to the reader's imagination. The ending is what makes a story memorable years later.

(Also, not a lad. )

Yes filler is almost always bad because it has to be completely stand alone from the main story line. They anime production companies need to fill in months of show content because the ongoing story is driven by the manga. They need to provide alternate adventures that don't provide meaningful character development or introduce any major plot events. Because of that they have to take an essentially lower quality approach to writing then a skilled writer would normally take. After all you might produce 6 months worth of episodes that have to have the characters end up exactly where they were when you branched off from the main story arc.

There are some exceptions to this I'm sure but the only one I can think of that I enjoyed was Full Metal Panic? Fumoffu which was more of romantic comedy side stories that took place between season 1 and 2 and where in many ways far more enjoyable then the main seasons.

Good story telling is at its heart about characters. Whether its their personal journey to reach their goals or potential, the journey to come to terms with their own choices in life, or it might be about the interactions between other characters the conflicts, humor, and bonding that results.

The story might take places on a space station during an interstellar war or at high school it all depends what the writer was to introduce as a back drop for the events. Take Supernatural that is about two brothers far more than it is about the monster of the week. Or early Naruto from 15 years ago when it first started back then it was about characters who was trying to be recognized by those around them and prove that with hard work you can catch up or even surpass a genius.

Theme is also important as it binds together the stories over a long arc. It provides reoccurring underlying context to be explored and reaffirmed again again.

Another good mark of a long running series is a willingness to change the theme and explore new areas over time. You can't keep the same underlying plot going forever without it going stale.

Lastly a lot of great writer agree that you have to keep the ending in mind from the start. The ending is something fans will always remember for better or worse. It doesn't need to tie up all the loose ends or achieve a happy ending for all characters but it must reach satisfying conclusion. The reader needs to feel they've completed their journey they might have still have questions and can speculate on how things will turn out for those involved but they should feel satisfied with the ending they've reached.