Cliche's can be fun for the Player!
The thing to remember here is that although a game may have numerous cliches, it is what it is, and a cliche itself is neither good or bad, it depends on how it is used. Every type of game would also fall into the category of cliche. Thus, cagetory = cliche. Oh noes, another RPG cliche. Oh noes, another beat em up cliche. Oh noes, another first person shooter cliche. Oh noes, another horror cliche. None of these by themselves are good or bad. What determines if they are good or bad depends on the individual player. It also depends on the mood of the player.
The point is, you can take any cliche, or category and make it fun, or make it a nuisance. Lets take a few off the top of Cabfe's linked list.
Sleepyhead Rule
The teenaged male lead will begin the first day of the game by oversleeping, being woken up by his mother, and being reminded that he's slept in so late he missed meeting his girlfriend.
Is being a sleepyhead necessarily a bad thing? As a story mechanic, it provides a meaningful and quick way to get into the introduction. Replace Mother with Sister and it will still be a cliche. Replace Sister with Father, Child, Grandmother, Robot Companion, Blabbering Fairy, and it is STILL a cliche. But replace the Character with a Non Human Wakeup Call and you get another set of cliches, each with their own set of story writing problems. Say you use an Alarm Clock. How do you introduce the main character to the player? Self Dialogue or Narration. Again, more sets of cliches. How about Amnesia? How do you communicate to a player quickly, in a way that is entertaining to the player what the main character knows about the world?
I'll take a crack at something more realistic. The first thing I do when I wake up is head to the bathroom and pee. How many games use urination as a way to introduce the main character? What kind of dialogue do you preset to the player? "Hello. My name is Ralph, and on this fine morning, I woke up ON TIME and really had to pee." Is that actually any fun for the player? "After I peed, I had to brush my teeth." The two problems here are how to make this fun for the player, and how to give the player meaningful dialogue that introduces the main character to the player and quickly establishes what they know of their world.
Honestly, I've never seen the "I have to pee" as a form of character introduction. The only game I can think of where you control the characters urination cycles is The Sims. Have you ever played an RPG game where you have to eat, drink, and manage the urination and bathroom cycles of every member of your party? Probably not, and if you did, it would become more of a nuisance to the player than enjoyable. Controlling bathroom cycles becomes as tedius as the "Press X to not die" cliche, but with zero sense of accomplishment. Thus, you can break free of all of these cliches and do something unique, but it will come at the cost of not being well recived by many players.
I cant get into a fight right now, I have to pee! I cant get into a fight with an evil overlord right now, I have to pee! What? The evil overlord is not willing to enter into combat right now cuz they had to pee? Then do this for EVERY battle? If a game were available where i was required to manage the urination cycles of characters, and a game that was full of well done cliches, I would choose the well done cliches over the urination cycle game every time.
End point is that regardless of what you do, you'll have a cliche in some way shape or form. Just make what ever you create to be fun for your players.