Saved from Development Hell: The project, until its 4th January 2012 release, was in development for 5 years, a period of time landmarked by at least one almost-total restart, several script re-writes, members of 4LS leaving/shown the door for one reason or another and a few art revisions. It also was very close to death within the first few months of its conception, resulting in the aforesaid restart.
Of the 21 or so developers at the end, only three were there from start to finish.
Troubled Production: Inevitable for such an ambitious fan-made project. Having to coordinate multiple programmers, artists, and 5 writers (one for each route), many of whom were working on the game only as a hobby and didn't even live in the same country contributed to numerous delays in development. There were also many internal conflicts within the team, leading to high turnover rates among the staff.
What Could Have Been: According to Word of God, there were massive amounts of content that were ultimately cut from the final version of the game. The following comes from snippets of interviews and Q&A sessions with the devs.
One of the writer's wordpress account has some writings that were considered in early versions of Hanako's route. Among them are Hanako's father saving her from the fire (which fits in with early character descriptions that only mentioned her father being dead), as well as a Left HangingDistant Finale involving a reunion between Hisao and a much more mature Hanako, many years after she vanished from his life following a second heart attack. Also, one of the entries involves a possible ending for a theoretical Misha path.
The final image of Hanako's good ending where the camera pans to inside a bakery window with two muffins sitting inside was originally meant to represent that Hanako has a bunin the oven, or in other words, is pregnant. This was scrapped in later drafts, though (Hisao very deliberately uses a condom that he happened to be carrying with him for unclear reasons), and the inside of the bakery is instead symbolic of Hanako and Hisao's future together enjoying the simple pleasures of life. This was most likely done to avoid Unfortunate Implications from seeming to promote Teen Pregnancy.
Also could be considered averted Fridge Horror considering how Hanako's condition would make pregnancy especially difficult for her.
Hanako's path was originally a "trap" of sorts. Going through it the only endings all result in death. In order to get a good ending you would have to play Hanako's path once, do Lilly's path, and half-way through you could court Hanako instead. The was scrapped due to being way to complicated to write and program, as well as a general desire to have the game develop in a more lighthearted direction
Originally, Lilly would have played the cello as a hobby, and her favorite song would have been Sarabande. However, this feature was cut and the song was instead changed to be the theme of the music box.
She also had a guide dog called Niji; after a while, however, the writers thought he added nothing to the story and ditched him.
She was originally supposed to be the oldest of 5 children in the family, with Akira being a younger brother. They eventually scrapped the other three siblings, gender flipped Akira and made her the older sister instead, although she did retain the male mannerisms.
Yuuko was originally Lilly's cousin, and not a librarian. Much of Yuuko's personality and role was given to Akira in the final product.
Lilly was originally half South African not half Scottish. Likewise, instead of Hanako turning eighteen Lilly was the one that was meant to have a birthday. They have it in Hisao's room, with Yuuko coming by and bringing alcohol.
In a very early version of Hanako's route, one of her bad ends would have involved Hisao having sex with a heavily medicated Hanako, which would have been the equivalent of date rape. In fact, her good end would not have involved any sex at all.
This wasn't completely scrapped. At some point a drunk Hanako hits on Hisao heavily, but he's Above the Influence and puts her to bed; and later after their H scene, Hisao is horrified as he mistakenly thinks that the sex with Hanako may have not been as consensual as he thought, and that's why Hanako is avoiding him in class. She corrects him and says it was all consensual.
Early bad ends past Act 1 would have involved Hisao dying, but they were ultimately removed because the writers felt that having to come up with convenient accidents for each death would feel too much like an Ass Pull. Hanako's writer wryly notes that he reconsidered killing off Hisao in Hanako's bad endings because he believed that the thought of a life without Hanako worked better as a Fate Worse Than Death.
Misha was originally conceived to be as bland and uninteresting as possible, so that players wouldn't miss her if she was pushed aside during Shizune's path. Very different from how she came out in the end, both in terms of personality (which also led to her popularity) and role - her presence and importance stay strong in Shizune's path. The revelation that she used to be more plain in appearance, before dying her hair pink and styling it in the characteristic drills, may be a nod to the old concept.
She was also originally planned to be blonde, and lacked her signature Drill Hair.
Miki was originally planned to have a much larger role in the game; among that, a short bonus route with her as the main character, showing some events from her point of view.
Several older sketches and drawings from 4LS members (both former and current) show ideas that floated around during development.
Two or three different school uniforms were considered throughout but the final design ended up staying close to the original sketch, even in the color scheme. One of the alternate designs (shown in the Art Evolution sequences after the good endings), with jackets and long skirts, would have been justified however, since the story originally took place in Winter.
Same with the hairstyles. The only heavy departure from the colored sketch is Shizune's hair color.
Other sketches show Hanako having suffered even more extensive damage from the fire on the right side of her body, with a blind eye and the leg supported by a crutch.
A compromise for Rin wearing a female uniform and keeping decency was thought in having her wear training shorts under the skirt. She also seems to have been envisioned as much taller at first. In general, while the basic design stayed the same, she was more feminine and delicate in appearance.
Shizune's route was originally going to be very different from the final product. But the original writer left 4LS due to internal conflicts with the rest of the staff and A22 took over in his place. And how was it like? It was quite more dramatic, had some more options (like Hisao giving or not a Kiss of Distraction to Shizune, or him asking Misha out for a date at some point - though she'd turn Hisao down saying "I'm not avaliable, sorry"-), Misha actually commits suicide and Shizune either gets close or downright crosses the Despair Event Horizon due to it, is hospitalised due to her health taking a nosedive, and in the Bad Ending she falls victim to Death by Despair.
Shizune also could says near the end that she could read lips, something that isn't stated in the final product.
The original version of the game was much more morbid, with death often being a part of the endings.
Kenji and Yuuko are confirmed to be dating in the earlier script. In the final product it's somewhat implied they were each others exes but it's never stated. One of Hanako's scrapped good endings would have them married and with a daughter named Karen, whom Kenji openly dotes on.
Emi and Rin were meant to pop up a lot more in other arcs, especially Lilly's.
Hisao originally was a Yuri Fan who thought Girl on Girl Is Hot, having at least two fantasies involving his friends; once with Misha and Shizune, and the other with Lilly and Hanako.