The thing about originality is that originality is judged from the reader perspective.
A reader will only consider a story a retread if it's similar to one they already know.
You see this effect particularly strongly in YA novels, because young children, almost by definition, tend to be less well read than adults. Take, for example, the Inheritance Cycle. The series takes the plot of Star Wars, the magic of Earthsea, adds a Pernese psychic dragon-bond, and drops it all on a bog-standard Tolkienesque fantasy world. But the vast majority of the middle-schoolers who read the book have not read A Wizard of Earthsea, or the Dragonriders of Pern. So True Name magic and psychic dragons are new and exciting, even though the ideas that inspired Paolini are decades old.
Now, many of the kids reading Eragon were probably familiar with Star Wars and Lord of the Rings. But how new something seems depends on more than just familiarity with previous iterations of the same concept - it also depends on familiarity with other things. A chihuahua and a poodle seem like totally different animals, until you put them in a lineup with a crocodile, an emu, and a walrus. Suddenly it become apparent how similar they are in the grand scheme of things. The same is true with stories. For a child, Eragon is a new twist on the story they loved in Star Wars, and it's not until they start to read other versions of the Hero's Journey that it starts to become apparent how little twisting it actually does.
The Familiar and the Strange
"The familiar and the strange" is a concept that I first encountered listening to the Writing Excuses podcast. The idea is that audiences need something that they can relate to, but they also need something new and interesting, and the key to keeping reader interest is to find the correct balance between the two.
The trick, though, is that every reader finds a different set of experiences familiar. If you divide up Inheritance like I did above as a combination of Lucus, Tolkien, Le Guin, and McCaffery, then for me Paolini is a mix of familiar, familiar, familiar, familiar. But his general audience finds this mix to be familiar, familiar, strange, strange. It's a good mix for them, and a terrible one for me. Meanwhile, the books that are a good mix of familiar and strange to me are going to lean heavily on strange to those kids. (Also, kids are drawn to repetition, and their balance of how much strange vs how much familiar they want is different, just as how they measure strangeness is different)
Any book that does as well as Harry Potter, Inheritance, or The Da Vinci Code is necessarily drawing the majority of its audience from people with less familiarity with the existing literature that they're built off of. That means that any book that hits the sweet spot of strangeness for millions of people is going to necessarily feel overly familiar to experienced readers.
There's more too it, of course
If I had some sort of magic formula for writing world-famous stories, I would not be going to work tomorrow. To be successful a story needs to tap into more than just a mediocre level of unfamiliarity. But I think that this explains in part why so often popularity and quality seem to be, if not opposed then at least tangential to each other.