Dummied Out: Analysis of the source code reveals that there were additional upgrades planned for Amethyst's Suplex and Shooting Star abilities: one to give Suplex a longer duration, and one to give Shooting Star its One-Hit Kill ability from Attack the Light. They are both fully functional, but aren't featured in the game.
Though Attack the Light is an obvious inspiration, the gameplay mechanics were more closely inspired by Alter A.I.L.A. and several games by RPG Maker developer Craze. In particular, the aversion of Arbitrary Headcount Limit was inspired by Czarina Must Die! doing the same.
A Friendly Irin has repeatedly referenced Trigun as a huge inspiration for the philosophy behind the narrative's grappling with violence and nonviolence.
Lapis Lazuli was actually considered to be a party member early on, but the developers couldn't come up with a fighting style that would've made sense for her. In the final game, she ended up being the shopkeeper and would allow players to escape from dungeons (except the Alpha Kindergarten and the final dungeon.)
Steven originally had several abilities that were cut: Pep Talk (a full heal ability), Lacrimosa (50% chance of revival) and a another variant called Grieve or Mourn which would have a 100% chance of reviving a party member. He also had Rallying Cry and an unnamed variant which was a better version. Connie had several multi-hitting attacks, an armour piercing attack and a skill called Feint which would lower enemy ATK + DEF.
Motivational Speaker was going to be a passive skill but was eventually deemed unnecessary and was kept as a badge instead.
There were originally plans to give Bismuth a Combination Attack with the entire team, but it was scrapped on the basis of being too unclear and overpowered.
Peridot originally had Rallying Cry and Pep Talk but those skills were cut when it was decided that all party members would be limited to 4 skills each. She'd also have a joke skill where she'd surf the internet to find out an enemy's weakness only to get distracted by Twitter for several turns; this got cut because A Friendly Irin couldn't find a good way to implement finding enemy weaknesses in addition to enemy stats already being shown by default.
The final dungeon would've been originally been a full on dungeon with twisted versions of the gems as enemies. This was nixed when it decided to have a Point of No Return and the Boss Rush idea emerged from there. In addition the room phantom was going to be Greg instead of Rose, representing the purest incorruptable thing Steven believed in; this was changed to Rose instead because the developers felt there was a lot of unanswered questions regarding Rose Quartz and that it made sense for Rose's personality to be a manifestation of Steven's corruption.
There was going to be a fakeout final boss where the player would fight Rose-Steven before fighting Corrupted Steven similar to Porky and the Masked Man in Mother 3. It was quickly cut due to being unnecessary and making little sense, because Rose-Steven being a room phantom meant that they shouldn't be beatable through conventional means.
early on, but the developers couldn't come up with a fighting style that would've made sense for her. In the final game, she ended up being the shopkeeper and would allow players to escape from dungeons (except the Alpha Kindergarten and the final dungeon.)