What are some of the causes? In short, you could say that it is the copycatting of literary mechanisms. People read books, they watch movies, or T.V shows they like and are bombarded with different narratives, and it doesn't take long to start and decipher the formulas at play. Just as archetypes were defined in early literature, new variations have bubbled to the surface and become more prominent. My least favorite of these, is the love triangle. The love triangle is commonly associated with young adult, or new adult, and centralizes on a female protagonist torn by the decision of two loves. So often you see a young female, often in their teens poised between the new guy (usually a bad boy) and the "best-friend" who she never realized was in love with her. I am not saying that love triangles are bad, but what I am saying is that their use in the past few years has been exceptionally bad. As with any literary mechanism, its use should at least feel unique. Try and approach something in a slightly different way than others of the time, or those that have preceded you. For example: avoid the love triangle as formulated in so many young adult books of recent years, ie: Twilight. Instead, consider how Diana Gabaldon used the same technique in her Outlander series. Ultimately, it is the same principal, just with a unique, and quite intriguing spin.
Next, the mysterious father. I am talking about the young hero, often raised in seclusion, before he/she is called to take up arms to save the world. And when he/she faces the antagonist, they discover that he/she/it is really their father and blah blah blah. Yes this was a shocker, when Darth Vader told Luke "I am your father," the shock was real...in 1977. So many books are compelling because of their twists, so think hard about how you want to twist the plot, and the reader.
Another example is that of the chosen one. There are easier ways of creating drama within a narrative, but it is not always easy to link your character to the action, at least not in a fresh, believable way. But please, stay away from prophetic (chosen one) mechanisms. Unless, you are going to do the groundwork necessary to raise your story above all of the rest. For starters, what higher power is/was responsible for elevating/choosing/christening this character, and to what end? Oftentimes a prophecy is injected into a story to avoid having to do all of that pesky back-story stuff. You know, that stuff that gives a story history, weight, and supports your story arcs and your setting. Consider this. Instead of making a character special because some unseen power has deemed them to be, make your character special because they desire to, or need to be. Make their elevation, or ascension to status of hero part of their story arc, but also make it a key part of their development as a character. If there is something about this character that makes them special, explore it, but also take the time to create a unique connection to that power/ability's source. One which will take readers off guard. After all, we all love a little surprise as we read a book.
Stay away from portals, or gateways to other worlds. I know, they're handy, but oh so overused! How many times can we take ordinary housewives, kids, or teens from the ordinary, mundane world, and throw them into some magical/alternate world, where they ultimately amass skill and prestige and save the world. Then they return home and carry on in their lives, all the while wishing they could transport back. This is become oh so cliche. Remember Edgar Rice Burroughs, the author of Tarzan, he used this literary mechanism in his book The Princess of Mars. In that story, John Carter, a civil war veteran is transported to the planet Mars, where he engages in a series of adventures. And that was first published in, oh, 1917, so move on.
Finally, and oh so cliche, is the retired hero who is called back into service, one...more...time. Because, heh, he is the only one who can save the world. There is really nothing I need say on this one, because quite frankly, I am surprised that it has been used as often as it has.
When writing your narrative, you need to keep these cliche mechanisms in mind. Consider that your average book consumer is very well-read, and has undoubtedly compiled a sizable library. Chances are, if you utilize these tired, overused mechanisms while writing your story, you will turn away not only potential readers, but may inspire some people to just put it down, unfinished. As an avid reader myself, I crave books that feel original, and if not, at least a fresh take on a popular idea. I want a book to tell me something in a new way, or take me down roads I haven't considered before. We all want twists, and turns that we cannot anticipate, or endings that catch us off guard. It is books like that that we lend to our friends and families. It is those books that we scorn sleep on a work night to finish, simply because we only have 60 pages left to read and are incapable of putting it down. It is books like that that we remember long after we finish them.