When it comes to cliches in my experience, focusing on them at all is probably when they become a problem. Like I tried writing a story that avoided them entirely, and in the end, I couldn't write the story I wanted to tell. Then again, try to embrace them, and... Well, anyone who obsessively embraces the "No cliche" banner could tell you the long list of what's wrong here. I can speak as a consumer, I do NOT
care if cliches are used if the over all game experience is immersive enough to keep my mind in the story. Perhaps I've grown desensitized to it, or maybe use cliches as a base before buying a game so I know what kind of experience I'm dipping my feet in before hand. After all, Vanilla ice cream is often regarded as being plain, bland, and uninteresting, but any condenser of vanilla ice cream could tell if a particular brand is well made or not. So if you choose to make vanilla ice cream, make damn sure you do it well, while adding your own special ingredients to the mix which hopefully strengthens the flavor.
So when making a visual novel, make your own ingredients, even if you are aiming give an experience that may have been told a thousand times before. Get it write, and you may just remind hardcore veterans of that genre why it was they fell in love with it in the first place.
Now that said, cliches are old. They've been used. People may already be tired of them. Don't become reliant on them. You don't need me to tell you this.
Here's a few solutions I could think of in alleviating a cliche.
Easiest way to fix it is to not use it, but come on. Lots of people love the school setting. If they didn't, it wouldn't be popping up so often. If you feel it benifits your over all game experience or artistic/story direction, by all means. Do it. Just make sure the school itself is treated with its own personality, just like the characters. No, I don't mean the setting literally talks to you, but what sorts of charm does it have in the eyes of the characters who walk its campus? Is it a new state of the art school erected in an old sleepy mountain town that's struggling to adapt to the modern world? Or has the general atmosphere become oppressive since a school shooting that occured a few years before your protagonist even enrolled? If the protagonist is a student, then the player is going to be spending a lot of time there. So make sure its fun and interesting to explore, even if the game is a comical, more character driven story. There could always be that one dusty room on the third floor which might be inhabited by a hobo who leads people to believe its haunted.
I see a lot of people grumble on and on about this. "Does it have to be Japan? What makes the country so important to the story that it can't be placed in an American, Australian, or German town?"
Yeah, lets face it. If you're setting the story in Japan just cause, you might as well set it anywhere else. But hey man, there is an answer here. Sociology. The Japanese view of life is quite a bit different from the western view. And its not any one huge thing that makes it like this. Its all the little things. Like this
for example. If you're setting a story in japan, make sure you drop your cultural ethnocentricity's at the door and adapt theirs... Unless you're writing from a foreigner's point of view. Bottom line, do you're research.
A pretty common one, and actually somewhat hard to pull off. The best advice I can put here is that you're character may not actually perceive themselves as an unhappy person. As was my case in middle school. I had depression from 7th grade to 11th and didn't even know it. Another piece of advice: If you want a discontented character, try to make it from a recent change in their life that they're begrudgingly trying to adapt to. You won't find many people who were unhappy for every second of every day in their lives. Rain clouds pass. You're character may even be a particularly positive one who is just going through a rough patch in life.
Certain character tropes:
If you see your character falling into a commonly used archetype, don't freak out. This is actually a fair starting point. In fact, its a good way to lead the player into a character's personality, only to surprise them with layers of depth they weren't expecting. In other words, "humanize them, bro!". Of course if you aren't willing on prowling around, studying people in their natural habitat, a good place to turn is surprisingly astrology. Doesn't matter if you believe it or not, if you figure out the perimeters of a character's sun/ascendant/moon, then you pretty much already have a functioning character. Sure, it may be just as lazy as using a character archetype, but its hard not to get at least relatable characters, even if they are presented in a more familiar, anime style of portrayal. (Then again, not every VN out there needs to be anime, those are just the ones I prefer.)
I guess to sum up my own pretentious creative beliefs, a cliche is like that toy in your collection that every child already owns. Are you going to play with that toy exactly how you saw other kids doing it, or make up your own game using it? Or do you want to get the toys nobody else has? -shrug- Kay, enough with vanilla ice cream and toys. That was only my point of view, and I don't claim these thoughts to be right or wrong.