This topic has mostly already been covered well, but I wanted to add a couple things. To some degree, this might be getting into the difference between "trope" and "cliche". The former is benign, and do not need to be expressly avoided. The latter could be defined as "what a trope becomes when it's sufficiently overused". Still, even then, having some cliche elements in your story is not a bad thing, because it's nigh unto impossible to avoid them completely, and it's not the same thing as the entire story as a WHOLE being cliche.
In terms of characters, and the OP's question, I think it's also important to point out the difference between - again - having some cliche elements, and the character as a whole being seen as cliche. Most main characters (in an RPG, or a sci-fi novel, or damn near anything, really) are going to have at least one or two cliche aspects to them, and there's nothing wrong with that. Just because a main character who was an orphan is considered cliche by many doesn't mean you can't do it, if that's what fits. What we DO want to avoid is having a "cliche character." Meaning, the ENTIRE character feels like a walking cliche storm. A young, brash swordsman, who was an orphan and doesn't remember anything about his past, who carries a mysterious talisman that seems to be reacting to the evil that threatens the land, also his village was destroyed right before the beginning of the game and he is cocky and rushes ahead but always does the right thing by his friends and (etc etc).... And it's not just about simply having those cliche traits, it's also about those things being the main - or even only - aspects of the character that really shine through and show the audience what he/she is all about
Ok, the brash swordsman that I just described IS an example of a walking cliche storm, and would probably be seen as such by many, but even in that case, it might be possible to still turn him into a compelling character with strong writing and execution.
Super cliche-ridden characters could work in a parody/comedy game, but if the story is meant to be taken seriously, then not so much. But simply having some aspects of the character's background/origin/etc. be "cliche" doesn't mean "the character is cliche".
And it's absolutely true that how one uses cliches is much more important than whether or not one has them in the first place. Jumping through too many hoops to try and twist part of a story around so that it "avoids cliches" can easily result in an overly convoluted mess.