Ok, I need to speak my peace. There are elements used in stories, because they work. Or because their aren't alternatives. A male protagonist isn't cliche, it's just that a great deal of the world's fantasy writers are males who can't write a female veiwpoint. I didn't say all, but its difficult to write from the viewpoint of the opposite sex. Does this make a male protagonist cliche? No. Honestly, you have a total of four options: male, female, nuter, or asexual. However, we can't indentify much with an asexual non-human lifeform, so they're not good candidates for a story (maybe a movie, they would work). Just because ideas have been used before, or are used quite often doesn't make them cliche. We have a limited array of things to work with in a story, and EVERYTHING has been done before, but that doesn't make it cliche. However, there are things that have been done THE SAME WAY over and over and over, like a Hero's Journey in fantasy, and "I AM YOUR FATHER" revelation, the prophesied hero who is going to defeat the dark lord, ect. They were once really good an original ideas. And they were just done by combining ideas that were already out there. It's how we combine our ideas that make them unique. You can have a very original story that involves an "I AM YOUR FATHER" revelation, but you need a new twist on it, that makes it feel fresh and new. You can also have a good original hero's journey story, but you're going to have to change it up quite a bit, for it to feel new.
To reiterate, just because an idea has been used before doesn't make it cliche. There are only so many ideas in the world, it's your spin on it that changes things. Using a cliche is a bad thing, in my opinion. If your story NEEDS the cliche, I say rework it. If you can't get around it, then put a new and original take on the cliche. There is a short podcast on this subject, which I think makes the point quite well, and it can be found
HERE Don't get me wrong, there are plenty of great games that have very cliched storylines. But what makes a game interesting to me is a new refreshing break from the classic RPG story.