If you're having trouble writing a character when you first start out, try writing a full history for them. Example: I'm currently working on a new project and struggled to get a solid grasp on what kind of character I want the romantic focus to be, so I've made a new document with details from their exact birth date and the hospital they were born in, it's relative distance from the childhood home, and the occupation of the parents. Even small details like what influenced their hair style, what they were like as a baby, toddler and child before teenage years. Not only will it give you a much stronger character, it will make all characters related to their development stronger as a result, which will end up making even your side characters very unique.
What this will do in regards to your plot is give more attention to finer details, allowing you to better fill out your transitional "filler-but-not-filler" scenes with interesting facts about the character. An example of one of these useless, yet still interesting facts is having a character possess a strong love for something very strange due to a childhood toy or memory. Let's say the character had a plush toy of an acorn with eyes, kind of Banjo-Kazooie style, that they carried everywhere when they were young. If this character finds an acorn during the events of your route, short story, or whatever form of writing you choose, then you can have this strange affection come to light by having the character gather acorns in their pockets. Whether you explain why they collect them while this happens or make the acorns a recurring motif is up to you, each have their own merits, as well as their own problems. Obviously this should only be done with important characters, you shouldn't write a full biography of a character's past unless they appear very frequently and help further the plot.
Also make sure to do your research on the disabilities your cast of characters each have. If you're writing Suzu, research narcolepsy look at possible dangers of the condition. If you're writing Miki, Emi, or another character with missing limbs, research the effects of amputation, such as phantom limb pains, or the causes and effects of limb deformation while in the womb for characters like Rin. If the condition has triggers, like epilepsy or cataplexy, do some research on what can potentially cause attacks and have your character follow certain precautions to reduce the risk of seizures.
Try to reinvent the wheel sometimes, too. Pretty much every route out there seems to have a trip to the city in it, don't feel obligated to do the same. Why not have your characters spend some time hiking in the forest, or exploring the town down the hill? You can do whatever you want with your story, and if you have no reason to visit the city, then you don't need to do it. You can even change the events of the source material if it leaves you with a better way to start the story. You might have Hisao visit the Nurse before going to class on his very first day at Yamaku, then only have him get out of the office as lunch starts. He can meet your cast before he even meets any of the canonical route girls, he may never meet a particular girl at all. There are absolutely no limits as to what you can do, so think big and think differently.
While you're at it, do some research on the finer details of rural Japanese architecture, wildlife, and culture. Yamaku is in a countryside setting, and the nearby town is likely full of old people due to Japan's ageing population. There will also be far fewer modern establishments like Starbucks, so find out more about older practices like onsen, izakaya, Japanese theatre, and traditional cooking styles, like making mochi in a barrel with a hammer. Knowing the local wildlife will add a lot to your setting, so include details about cicadas chirping, what kind of trees are around (describe them by their appearance, not name, unless your character is a tree enthusiast) and the different bird sounds that can be heard at different times of the day. You may be writing for a predominantly Western audience on these forums, but don't be afraid to avoid Western culture unless it's essential to your plot. Public displays of affection are a good example of this. Generally, these displays are frowned upon in Japan, but you're likely writing a romance story. Screw what the rules of society say, have your characters kiss in public if it makes sense for them to do so, it makes for a more interesting story.
The last tip I'll give in regards to general writing quality is to make dialogue more interesting. Stop caring about grammar so much, it only serves to make speech sound overly formal, even in formal situations. Don't be afraid to use words that don't exist (but sound like they could) or invent slang either, as long as you explain the definition of the new word very clearly. The main thing you should try to do though is gather a few friends and assign characters to read aloud (or do it alone, it's fun being crazy sometimes) to ensure that conversations actually flow properly. Hell, improvise the lines sometimes, adding your own personal flair to it will only make your dialogue sound more natural, and natural is good. Try to avoid having any two characters sound the same. Groups of friends only work because there are enough personality traits to keep things interesting, otherwise you could sit in your room and have conversations with yourself all day and never notice the difference. Groups tend to have a strong leader, as well as a weakling who follows everyone else without question. Try to put this across in their dialogue, clearly define what traits somebody has, whether they be a sexual deviant, a quiet introvert, or a straight-up dick, it'll make your characters lines more memorable and keep them fun to write.
To round it all off, don't be afraid to rewrite things. Multiple times. I've rewritten the first chapter of this new project at least six times already, and I've sent myself back to the drawing board to make some changes and give myself a better set of tools. You should never put something out unless you are absolutely sure you want to release it, because if you don't want to release it, then it isn't your best work. You should constantly be trying to write something better than your last chapter, though that isn't always possible due to the existence of slower plot development phases. Not only will this help you grow as a writer at an accelerated rate, but it'll keep your readers interested and have them discuss possible upcoming events and plot twists. You'll also feel a much bigger sense of accomplishment on completion, especially if you read your first and last chapters back-to-back, because you can very clearly see how much you've grown over the time you spent writing.
Whew, didn't think I'd write this much when I started typing this post, but there it is. Obviously this is all just how I do things, different processes work for different people, so if these tips don't work for you then don't be discouraged. Simply pick your head up and try a different approach, and remember that there's no magic formula for writing a better story. Oh, and if you've never written anything over 5,000 words then start small, don't start a route and expect it to go smoothly. Things will fall apart. On that note, I'll stop rambling and let you get on with your day.