At first, Austin didn't bother to come up with a reason why Yado created the vaccine because "[LISA: The Joyful is] a video game [that] lacks completely credibility". He eventually canonized the idea proposed by Charles O. Ward in a thread on Twitter that Yado's god complex drove him to make sure that he wouldn't turn into a Joy Mutant himself.
RT, Jack, Garth, Beastborn, Sonny, and Yazan are all party members created by Kickstarter backers. Notably, there were going to be four more backer party members, but they fell through for unknown reasons.
Copiously Credited Creator: Austin credits himself as writer, artist, creator, and musician — just under different names each time.
What Could Have Been: A consequence of the game's development being mostly open and taking place over two years is that a lot of story and gameplay elements ended up dropped during production:
Rick, Sticky and Cheeks were all at one point recruitable party members, and Rick and Sticky still have unused battle sprites and animations in the game code.
Early gameplay trailers hinted at a completely different main plot, with Buddy asking Brad and the uncles about a mission of revenge.
Columbo has enemy battle data in the final game code and an unused battle theme in the soundtrack but isn't fought in the game proper.
An early teaser image◊ shows sprites for multiple party members and characters, a few of which go unused.
Iori Stevens has a few extra unused sprites in his file, implying that he was originally planned to be a recruitable party member.
A gameplay feature that ended up being cut for time was specific side quests for different party members, in the end, Bo was the only one who ended up with his own side quest, searching for his lost brother.
A minor change, but an early teaser shot◊ of the Salvation Rangers implied that Dick was actually yellow.
There were initially supposed to be ten Kickstarter backer characters, but four of them fell through for one reason or another, and the game only ended up with six (Beastborn, Garth, RT, Yazan, Jack, and Sonny).
A completely different set of party members are listed in the game's data as Joy Addicts, but due to either a bug or deliberate removal, the variable that prompts their withdrawal status never switches. These include Rage, RT, Garth, Sonny, Birdie, and Fly. A game mod exists that allows you to allow them to suffer withdrawal again.
The game was initially titled "The Last Matador", and interviews with Austin Jorgensen imply that it was not originally connected with LISA: The First until well into development.
In fact, Austin's original concept for this game was a Fist of the North Star-type setting in which a bunch of ripped dudes beats each other up, then he started to get into the deeper aspects of a world without any women.
The fight against Sindy Gallows in LISA: The Joyful was added last minute, which implies that he was originally supposed to stay dead and the cultists that killed him was the real fight.
The pre-alpha gameplay footage shows a lot of things that didn't make it into the game. Aside from the aforementioned Ricky and Cheeks as party members, the trailer also shows them having a team attack that implies that moves can be done with certain party members in the same party, a party member named Hawk that is nowhere to be found in the final game, a sneaking mechanic that seems to be a precursor to the assassinations Buddy can do in LISA: The Joyful, proper battle backgrounds instead of the in-engine generated ones, and more blatant foreshadowing of Dr. Yado.
Austin Jorgensen had mentioned in interviews that he originally wanted to put several reference characters in LISA (mentioning the USA Sports Team from The King of Fighters specifically), and sprites for quite a few of them do exist in the sprite sheet, but in the end none made the cut save for Expies of Lucas, the Mario Bros., and Everdred.
Austin stated that Rando was originally going to be one of Brad's biological children and that Hawknote Not Hawk Hollywood, but a different, scrapped character was going to compete with Brad to gain Rando's trust, and eventually control the Rando Army. This subplot was scrapped but a Dummied Out sprite references it.
The sprites for Mr. Beautiful and his gang appear in the artbook for The Painful, implying that they were going to debut in that game before ultimately being Refitted for Sequel. The book is the only place where the gang's full name, Beautiful Baby Boys, is revealed.
Write Who You Know: Austin Jorgensen has stated in interviews that the idea behind The First (and, later, Brad in The Painful RPG) was based on an ex-girlfriend who was scarred by memories of her abusive father, as it had made him realize how much memories can affect people.
Additionally, he has also stated in a Twitter post that Brad Armstrong was both inspired by and named after his late father, Brad Jorgensen, who was stated to be a great father, and hard-working Determinator when it came to getting anything done. Above all else, Brad, the character, pushed himself to his limits to help those he cared for, much like his basis.