The updated character designs for returning characters came from wanting to take advantage of the higher screen resolution and to give the game's characters more detailed and matured identities since the first game, rather than just making another Sonic The Hedgehog-inspired game. Lilac's new design had influences from Mega Man X's armor upgrades to show how much more responsible & experienced she had become, while Carol had minor updates showing she hadn't changed too dramatically, and Milla's more cleaned-up jumpsuit design showed how she grew to take care of herself since her tattered appearance in the first game.

Many of the new characters, story and new region of Parusa are inspired by Filipino culture & mythology. Examples given by the developers include Merga's armor being based off ancient Filipino armor, the characters of Aaa, Captain Kalaw and Askal being based off Philippine animals such as the tarsier, Rufous hornbill and askals respectively, and the ancient super-weapon Bakunawa being based off the mythological sea serpent of the same name.

There were originally plans to include a sidequest to restore Lilac's treehouse after it's destroyed in the beginning of the game, which would have required its own system of saved variables in the save files in order to have progress carried over.

It would've begun by talking to the NPC Wallace in the Singing Water Temple hub area who would ask the player to talk to Foreman Mun in Shuigang, who would assess the damage and give the player a price quote, which would be a ridiculous amount that the player wouldn't be able to pay at that point in the game.

So the player would either pay the amount later or recruit the extra labour he asks for, and then the player would go ask Lilibeth in Parusa to help rebuild the treehouse, which she would accept after the player does something for her.
The questline was cut due to time constraints and the extra work that would've been needed to implement it.

There were originally plans to increase the amount of potion and item slots, but the developers weren't sure how to implement it and had concerns over the game breaking if the player stacked the same potion into 10 slots instead of 5.

The Aqua Trooper enemies were based on lava sentinel-esque enemies from an old RPG project that the game's creator Sabrina DiDuro never finished.

Photos of the spinning-top toys Beyblades were used as reference when designing Carol's Jump Disc.

Neera originally wasn't planned to be a playable character, but after seeing the redesigns of the characters by Tyson Tan including Neera's new design, the game's creator Sabrina DiDuro was so impressed she added Neera as a playable character.

The names for the stages Bakunawa Chase and Bakunawa Rush are homages to Final Chase and Final Rush from Sonic Adventure 2.

The background of the stage Shenlin Park is inspired the first prototype screenshots of Mega Man X, also known as "the white city prototype".

Due to the increased scope of the game, Freedom Planet 2's creator Sabrina DiDuro briefly considered the idea of splitting Freedom Planet 2 into two parts similar to Sonic the Hedgehog 3 and Sonic & Knuckles during development, but she and her team at GalaxyTrail committed to keeping it as a single game despite how long it would take to complete it.

The game's creator Sabrina Diduro has stated that the reason Classic Mode isn't available until it's unlocked by beating the game, is because of how much effort she and the team at GalaxyTrail put into the story and how it is much more integrated into the game compared to Freedom Planet. However, there is a cheat code to unlock Classic Mode early, which is done by entering the Sonic the Hedgehog level select code at the title screen.