Anime First: One of the earlier examples. Some fans claim that the whole idea of anime as a medium of its own and not just an outlet for manga started with this series.* It actually started much earlier in the early-mid 1960s with Toei's first animated TV series Ookami Shonen Ken ("Ken the Wolf Boy"). It was one of the first ones to become popular, however.
Creative Differences: Yoshinobu Nishizaki and Leiji Matsumoto both claim they are the sole creators of Space Battleship Yamato. (The court system has sided with Nishizaki.) Both have made their own separate Yamato projects* the short-lived Yamato 2520OVAs from Nihizaki's camp, and Matsumoto's Great Yamato manga between 1983 and their settlement in the 2000s.
A bigger example was that the number of episodes for the Bolar Wars was originally 52 episodes, but was reduced to 25.
What Could Have Been: Before Leiji Matsumoto joined the project, the Yamato wasn't even in it, instead there was a ship made from a hollowed out asteroid called the Icarus. The show was originally pitched as essentially "Lord of the FliesIN SPACE!", with the crew suffering a catastrophic breakdown in discipline during their voyage through deep space. Virtually the only thing both versions had in common was that both involved a quest to find a planet called Iscandar. Fortunately, many of the concepts Matsumoto threw out when he took over were later used to make Infinite Ryvius.
The short-lived Star Blazers comic book by Argo Press makes an homage to this by giving the Earth Defense Force an asteroid base called Icarus.
The asteroid Icarus makes a cameo in Be Forever Yamato. Its hollow core is the hiding place for the Yamato, and the release of the ship shatters the asteroid.
Also, the first season was originally supposed to be 39 episodes instead of 26. The extra 13 episodes would have been used to introduced a new series character named Captain Harlock.
Before the series was cut down to 26 episodes, Mamoru was supposed to have become a Space Pirate calling himself Captain Harlock instead of being found alive on Iscandar.
...and he's in most of the promotional materials produced from the early drafts of the script, the first novelisation and it's in both manga versions - Matsumoto's and the "official" tie-in version... and there's no implication about it - it's outright stated, and he's treated as a major character! In said novelisation there's an even bigger shock that didn't make the final cut: Captain Okita is his father... though anyone who's seen Matsumoto's manga version of the WW2 Arcadia of my Youth flashback might have had a suspicion or two, given the character design for the elderly Harlock in the framing story...
Resurrection and Rebirth are acturally spawned from the same draft for a Yamato movie in the 2000s.