In an interview with the game's producer/scenario writer Hiroyuki Takahashi and director Shugo Takahashi published in the 1993 Megadrive Fan Attack Special book, they stated that the enemy "Paste" (called "Bubbling Ooze" in the English localization) was originally going to be named "Slime". Its name was not included due to copyright issues, so they tried other options to name it like "Ooze" or "Gel", neither of which got picked. They later came up with the name Paste, while the English release gave the enemies the unused name "Ooze". It's possible that 'Slime' couldn't be used due to a copyright for the iconic Dragon Quest enemy of the same name.
Contributed by ProtoSnake
According to the game's development team in an interview published in the Megadrive Fan Attack Special book in 1993, originally the Achilles Sword could cast Bolt, but if it was used against Talos, he would absorb all the damage and it would not hit the surrounding enemies. The team later changed this so Talos could not be targeted with magic at all.
Contributed by ProtoSnake
In a June 1993 interview with game's producer and writer Hiroyuki Takahashi published in Dengeki Megadrive magazine, he was told about Shining Force II getting a lot of pressure for being better than the first Shining Force game and Shining Force: The Sword of Hajya (released in Japan as "Shining Force Gaiden II: Jashin no Mezame"). He commented:

"Yeah. I always feel like we’re “battling” with the previous games, so to speak. That’s why we talked a lot together as a team, about how to deliver a satisfying ending for players. We’d built this story up for them, from the opening to the mid-game climax, so we knew their expectations would be running high."

"Finding the right tone for that ending has taken a lot of trial and error. One day, as I was working on it, my brother Shugo sat down beside me and quietly said, “Seeing as this game has turned into such a big production… I want to cry at the ending.” I then spent about a month thinking about how to do that. I came up with something, but deep down I wasn’t sure if it was a good idea to do that to players at the end of the game. I showed the staff what I’d completed, not knowing what they’d think. Then one of the staff spoke, with tears welling up in their eyes, “This is really good!” So yeah, I’ve got some confidence in the story this time."


Later in an August 1993 interview published in the same magazine, Hiroyuki said the team objected to the idea of having an ending that would make people cry and would not include it in Shining Force II.
Contributed by ProtoSnake
After defeating the final boss Zeon, when Mitula disappears with the jewels of Light & Evil, her theme song "Water Goddess Mitula" fades out, then plays "Panic" when the Ancient Tower is being sealed in the International release of the game. But in the Japanese version, the "Water Goddess Mitula" theme plays out until Bowie and the others escape the Ancient Tower. The International version likely adjusted the timing of those songs to fit the situation of the cutscene.
Contributed by ProtoSnake
In a 1993 Dengeki Megadrive interview with the game's producer and writer Hiroyuki Takahashi, he was asked what was the basic difference between Shining Force I and Shining Force II? He responded:

"The first Shining Force was a game of armies battling armies. In Shining Force II, it doesn’t have that rigid “troops” feel so much—it’s more of a swashbuckling adventure. For example, say your team is traveling by wagon. In the first game you’d basically proceed straight to your “true enemy”, but in this one, you might get waylaid by random monsters along the way. In that sense, Shining Force II doesn’t feel like a game where you’re simply trying to defeat the big bad guy at the end."


Hiroyuki also stated that he intentionally changed the way the game's story progressed, noting that in the first Shining Force game, as soon as the player leaves town, they're drawn into a fight. He felt that players saw this immediacy as too linear and forced, and decided not repeat it with the second game.
Contributed by ProtoSnake
If a character has been inflicted with confusion, there is a chance that they will not attack either the select enemy nor themselves; the game will instead claim that they are playing their Game Gear, and that Shining Force Gaiden is a great game.
Contributed by ProtoSnake
Kiwi is likely inspired by the Japanese kaiju character "Gamera". Both characters share a very similar appearance, can both fly through the use of rockets in their legs, and both breathe fire.
Contributed by ProtoSnake
In the Japanese release, the credits featured several spelling mistakes that were fixed in the English release.

PROGRAM -> PROGRAMMERS
GRAPHIC -> GRAPHICS
MUSIC COMPOSE -> MUSIC COMPOSER
DIRECTERED BY -> DIRECTED BY
Contributed by ProtoSnake
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At the end of the game, where the protagonist kisses Princess Elis in order to wake her up, the Japanese version shows a a portrait of them kissing that appears on screen suddenly, but in the English version the image appears in an animated transition. The border was also removed for unknown reasons.
Contributed by ProtoSnake
Several alternate palettes for enemy sprites are unused. The palettes would create differing forms of the Bat, Chaos Warrior, Dwarf, Goblin, Minotaur, Orc and Worm.
Contributed by ProtoSnake
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After completing the game, a secret battle can be selected. The stage is laid out in the shape of Sonic the Hedgehog wagging his finger.
Contributed by ProtoSnake
There is secret fight with all the bosses, plus 2 prism flowers, and without the Kraken. To access this fight, you must beat the game and wait until the end credits finish.
Contributed by Outofmind23