Well, I think those three things all have different criteria for what constitutes a "good ___". But since you lumped them, I'll be a bit more general then.
Story, characters, and art. Now before you say that's a cop out and I just listed everything, well, you're right. But I'll elaborate on each a bit.
You typically either have character driven or plot driven stories. To accomplish either, the main driving force needs to be compelling. That's not to say a story can't have a mix of both, but neither can be weak. If the story is interesting but the characters are weak, there's less incentive for viewers to care about the story. If the characters are interesting, but the story is weak, it's hard to justify continuing to care. What this boils down to for me personally, is that you can't have one without the other regardless of the focus/driving force.
You can't ignore the visuals in an inherently visual medium, so I believe the art is also key. I think you need art that reflects or enhances the story and characters well. I'll give an example with one of my favorite manga series, Sunny by Taiyo Matsumoto. The art so perfectly conveys the emotion and captures the mood that the world/art becomes a character of its own at times. I'm not saying the art has to always be of the highest "quality" or that it adheres to any particular style as long as it suits the work. I have enjoyed many different works with extremely different art styles and "quality". Art is likely the most subjective part of the experience for people when talking about anime/manga/VNs.
tl;dr It's all subjective so just enjoy what you like and tell everyone else they have shit taste like the rest of us do.
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