Again if cliches were so "horrible" why do the masses still keep it popular? it's an never ending loop. fictional story telling is full of cliches, the audience complain and make rage/troll comments on it, the cliches still pop up left, right, up, down, and centre. I was discussing this on another thread actually
There's a narrative that cliches must be avoided at all costs, but I'd say avoiding a said cliche without setting your story to back it up is even worse. Don't like the idea of main hero hooking up with main heroine? Okay. Main hero hooking up with some other character that had little to no screentime despite heavy hints of mutual feelings between the two main characters? Sorry, but no. You can put all the twists in your story that you want, but it has to add up in the end.
Game of Thrones has a bunch of twists and turns that makes it very hard to predict where it's going. But most of what I've seen still adds up to this point. I can say I wasn't expecting something, but I can't say it came out of nowhere.
Compared to other shonen manga, I'd say Naruto and Sakura are not that cliche. Most manga has the heroine more or less liking the protagonist from the beginning but refusing to admit it, and it's generally fairly predictable they will end up together. NaruSaku started out with a heroine who didn't like him at first, had the main hero put aside his own feelings for her, time taken to show their personalities mesh well together, and use previous generations to set up what should have been.
And just because something's different doesn't mean it's a good idea. You could end a story where the bad guys win, but I doubt many people would gravitate towards that. You could have a story about realistic martial arts and near the conclusion hint at what we see in video games. I could probably think of other things, but there's a reason so many formulas are repeated: when done right, THEY WORK.