In the introduction the scene of Olga's cooking is longer: it shows Godo playing with her remote control and accidentally causing her to spill the dough she is making. (P. 53)
There is a scene with Olga reminding Godo to turn her off for the night before going to sleep. (P. 66)
A meaningful episode shows Olga and a teenage Godo seated together before a computer screen, studying. As in the rest of the introduction, there is no dialogue, so it is not quite clear who is teaching whom, but it seems that Olga does the explaining. Suddenly Godo kisses her on the cheek. Her confusion makes the screen fill with fireworks for a moment, then she gives him a motherly hug. (P. 64)
After the episode of Godo's training where he has to dodge jets of flame, his burns are treated by an automatic medical system similar to the one we see later inside the Space Shark (P. 104) . The scene was clearly removed to avoid repetition.
In the first part of the film Godo never as much as speaks to any of the other cadets. But in the storyboards there is a scene that shows him talking to his classmates. He tells some friends about the beautiful girl he met, they explain that it must be Lena, the President of Senate's daughter, laugh at Godo a bit because he does not understand social hierarchy, and warn him not to fall in love with a girl from the nobility. Lena's country house is also mentioned. (P. 132)
The scene of Olga's jealousy in the storyboards continues to show her before a mirror with a fashion magazine, striking a pose, then trying to paint her lips. She does not know how to use lipstick, and ends up smearing it all over her chin like clown's makeup. (P. 194)
Godo's conversation with Lena at the waterside is longer. Lena explains why it is forbidden for space pilots to enter the park: if they see how beautiful the Earth really is, they will not want to leave the planet to go on their missions. (P. 185)
At the camp there is a scene with a workers' family talking about earthquakes and planning escape. Black Jack listens in to the conversation over a hidden microphone, then gives an order to move everybody from that sector to another. To himself he adds that he is sorry for the workers but has his job to do. (P. 240)
Before the Space Shark arrives at Lacrimosa, in the storyboards there is a fight between two comical-scary alien monsters. So when Ban appears brandishing a gun and calls the monsters to order, his angry tone is perfectly justified. In the film Ban's lines are unchanged, but the fight itself is cut. (P. 336)
As Matthew Whiteley pointed out, the two monsters also appear during the opening credits of the 1980 Astroboy (Tetsuwan Atom) TV series - Astroboy fights them (many thanks to Matthew for the screenshots!).
The ant monster.
The red monster.
Ban also has a wife. A very remarkable character, Angra resembles a giant mole in a dress, several times larger than her husband. Her favorite occupation is digging cellars. (P. 344)
This lady actually made her way quite far into the film's production - some art books show a color still of her, under the name of Mogue. Presumably her appearances were cut after the film was completed.
There is a music scene missing which explained why Crack introduces himself as a cowboy: when Godo and the others come to talk to him, he is herding giant slugs, playing pipe. (P. 366)
There is another comic relief scene with Ban offering his guests a local fruit or vegetable that looks exactly like Saruta's nose. The fly that annoys Saruta also makes an earlier appearance here. (P. 346)
Life on board the Space Shark includes the three aliens having a meal. Poox sucks on something like a kalian, Crack eats popcorn littering all around him, and Pincho tries to sweep the floor clean. (P. 383)
The comical scene is balanced by Godo's conversation with Saruta about destiny: he is chosen to save the Earth ("By the Senate?" - "No, by fate"), and confronting the Phoenix is just another test... (P. 389)
As the Space Shark is preparing for battle with the Phoenix, a "Fasten your seatbelts" sign lights up. (P. 462)
The Phoenix's revelations to Godo are a little longer. When Godo refuses to believe the Earth is a living being, the Phoenix points out that bacteria in his body have no idea their host is alive. (P. 596)
In the storyboards soon after arriving on the idyllic planet Godo asks his companions to help him repair the spaceship. Crack angrily demands wages. The next episode shows Crack hammering at the ship's side. He lays down the hammer and tries to play his pipe, but the pipe sounds like a hammer. (P. 602)
Godo's conversation with Olga about going back to Earth is included in this scene, as Olga works on the spaceship, and Godo contemplates a cabbage-like vegetable.