The Chronology contains five unused story concepts for the Saturn Madou Monogatari written by former Compile employee Kenji Oda. All of them are considered canon to the Chronology:
The first story candidate would have involved more Jewel Guardians, akin to those from Madou Monogatari: The Final Test.
The second story candidate would have seen Arle's kindergarten teacher calling her to defeat some monsters, and would have ended with a rematch with Fudoushi.
The third story candidate would have involved a treasure hunt at a magic school's vacation spot.
The fourth story candidate, "Catastrophers", is significantly more detailed than the previous potential plotlines. After a series of prologues in which Arle battles Fudoushi yet again, Rulue battles her mentors, and Ragnus battles Rune Lord in the past, focus shifts to the battle between Arle's friends and a doomsday cult named the Catastropher Seven. Rulue's father and Schezo's step-brother would also be involved.
The fifth story candidate is Shin Madou Monogatari itself.
"The Day the Puyo Disappeared", an event on the Chronology that is marked as being a summary of an unreleased game, was originally reserved for Arle no Bouken: Mahou no Jewel. The obscure Game Boy Color RPG was originally going to start a mini-arc where Arle makes an offhand comment about "not wanting to play forever" that inspires Dark Prince to try to undo the age freeze that he enforced on Arle's world. This plotline would have bled into Pocket Puyo Puyo~n and Puyo Puyo Gaiden: Puyo Wars. Schezo Wegey, among others, would've been aware of the fact that nobody ages. There's no trace of any of this in the final game.
Pocket Puyo Puyo~n, as mentioned above, would've also been connected to the Chronology. The scenario writer, Kenichi Ina, stated that the staff wasn't very receptive to the idea of such a serious story, which likely lead to this idea being scrapped.
Carbuncle would have been kidnapped by the Dark Prince in order to gain enough power to undo the time freeze.
It would have been revealed that the incarnation of Arle Nadja seen in the Puyo Puyo games thus far was only one-half of the incarnation of Arle Nadja seen in Madou Monogatari. Arle's soul - the other half being Doppelganger Arle, would have wandered the void between dimensions for hundreds of years (500 years, to be exact). Upon his initial discovery of Doppelganger Arle's existence, Dark Prince would have arranged for an encounter between the two Arles to resolve the issue of both existing. The Pierrot costume, in addition to concealing Doppelganger Arle's true identity, was also designed to seal her powers; this would have explained why Pierrot does not have access to a Super Attack during Arle's first encounter with her.
Unused Game Modes and Features
The 8-bit Puyo Puyo was originally set to be a Disc Station release. According to Niitani, the decision to develop for the Famicom Disk System came because the peripheral was failing and thus Nintendo would be less concerned with the similarities between Puyo Puyo and Dr. Mario. The oldest concept was a domino-stacking game, hence why the 8-bit versions have six colors.
The prototype of the arcade Puyo Puyo contains six Puyo colors. The sixth color (teal, instead of the MSX game's gray Puyo) was Dummied Out, but hackers have discovered that both the first arcade game and Puyo Puyo Tsu are still capable of handling it. The strangest part? It is actually the third color internally.
Allegedly, a version of the first arcade Puyo Puyo with Endless as its main mode saw a location test and performed badly, leading to the competition-focused final game.
The Mega Drive version of Tsu has assets of a Nazo Puyo Mode that was finished and implemented into a handful of later ports.
There were several characters considered for the Saturn version of Tsu that didn't make it into the final game: Wraith, Jaan, Siren, Kerogga, Komori Gal, Barbegazi, Tyranno, Gorgon, People Rot, Ghost, and Wizard. Aside from Wraith, Jaan, and Barbegazi, none of these characters ended up appearing in a Puyo Puyo or even Nazo Puyo game. What's more, some of them like Komori Gal and Kerogga would never appear beyond their debut game.
In a similar vein, Pocket Puyo Puyo~n was originally going to feature every character from the original Puyo Puyo arcade game, Puyo Puyo Tsu, Puyo Puyo Sun, and Puyo Puyo~n, in addition to Doppelganger Schezo, Dark Witch, Black Kikimora, and Veneris and Saturni from Arle no Bouken . Whether by coincidence or in direct response to this idea falling through, Puyo Puyo Box features all but the aforementioned Arle no Bouken characters in its Scramble Mode (Plus a few more in Quest mode).
Just like its mainline predecessors, Yo~n was originally intended to have an arcade counterpart, but it was scrapped partway through development. That said, the artwork meant for said version was still fully developed and can be found in Compile's Puyo Puyo~n Compile Art Gallery CD-rom, and if the aforementioned artwork is of any indication, it would appear that Ragnus, Incubus, Minotauros, Honey Bee, and Momomo (characters who were planned to be playable in all versions of Yo~n, in addition to its Game Boy Color Pocket incarnation) were set to be playable in this arcade version.
This can even be taken a step further in the case of Momomo, who ended up being an non-playable character in all finished versions of Yo~n.
Kazunari Yonemitsu apparently had ideas for up to nine episodes of Madou Monogatari, with a "River of Time" being a plot element in the planned Episode 6.
There were plans for a Madou Monogatari 0 which would have covered Arle's birth. Specifically, Arle would have traversed her mother's womb and fought off disease-like enemies attempting to botch Arle's birth.
Carbuncle was originally going to be a baby fox-like creature, rather than a rabbit-like creature.
An early concept of Ringo◊ originally depicted her as a Magical Girl. She was accompanied by blue and yellow-colored companions to make up a Magical Girl Trio, making up the original concept of Puyo 7's ARS. One can infer that this concept art may actually have been the basis of 7's Transformation mechanic.
Puyo Puyo Tetris was supposed to immediately follow Puyo Puyo 7, but unspecified factors caused Sega to hold off on the game and release 20th Anniversary in the meantime.
According to an interview in 2017, Current series producer Mizuki Hosoyamada revealed that there were plans for a Puyo fighting game at some unspecified point in time, but the higher-ups at SEGA put a stop to it.
According to a Twitter user by the name of Kido_pyu, Tokuma Shoten (the Japanese publishing company who released the Famicom Disk System Puyo Puyo) had originally approached Compile, pitching that of an full-blown ongoing Puyo Puyo anime series to them shortly after the release of Tsu. However, the president of Compile at the time refused the offer, stating that he would like for all the animation for such a series to be done in-house at Compile. Unfortunately, Compile had little to no resources to take on such a task, resulting in the idea never truly coming to fruition. It should be noted that in 1998, Compile did release a series of shorts based on their various IPs at the time (with Puyo Puyo being among them), most likely being the closest they had ever come to accomplishing that goal. Kido_pyu is of the opinion that had Compile taken up Tokuma Shoten's offer, they could have just given them (Tokuma Shoten) the go-ahead to animate the Puyo Puyo anime series for a limited time while they themselves (Compile) kept the series' copyright, and then animated the series themselves later down the line instead of totally turning down the offer outright.
Compile had ideas for a Puyo Puyotheme park, of all things. It's unknown whether plans were actually being set in motion, or it it was just another of the company's less-than-realistic goals.
Puzlow Kids' existence implies that Sega had plans to release ports of the first arcade game in the west mostly intact. There's Wild Mass Guessing about why it didn't release outside of Japan (much of it involving the English arcade game), but no concrete answer. Admittedly, Several fans are thankful that, aside from the name change from Satan to Dark Prince, Puzlow Kids' naming conventions died with it.
According to one of the Japanese guidebooks for Tsu, Compile was going to try to get Super Puyo Puyo released overseas before they were approached by Nintendo for Kirby's Avalanche.
Current series producer Mizuki Hosoyamada wanted to push for 15th Anniversary (his first game) to be released overseas, but didn't because of concerns about recouping localization costs.