Beam Me Up, Scotty!: The iconic "Good Morning, Crono" appears on a bunch of wallpapers used to promote the Nintendo DS version, despite it being one of the lines that was altered in the new translation.
Breakthrough Hit: The game's soundtrack was this for Yasunori Mitsuda, resulting in him becoming an in-demand composer in the Japanese gaming industry and being one of his most acclaimed works in general.
Deleted Scene: For some reason, the Steam release and the mobile releases its based on remove the video cutscene of Crono, Marle and Lucca walking into Proto Dome and encountering Robo's derelict body.
Director Displacement: Ask any players familiar with the game to name a creative lead who worked on the game, and they would most likely answer artist Akira Toriyama and composer Yasunori Mitsuda first, with writer Masato Kato coming in second. The game's director, Takashi Tokita, remains relatively unknown outside of the cult fanbases of his other directed games such as Live A Live and Parasite Eve.
Late Export for You: Up until the DS version, the game was never released in Europe, nor Australia.
Urban Legend of Zelda: There were many rumors of about non-existant content, most often about ways to allegedly save Schala from her unknown fate.note A line which originally meant "talk to your allies for help with sidequests" being translated as "someone close to you needs help... find this person, fast" didn't help matters. This is the reason why this was at one point known as "Schala Lives!"
Several locations were cut from the game. The most infamous of these is Singing Mountain (aka Chanting Mt), a prehistoric dungeon whose music still remains in the game data (which was eventually used for a different location in the DS version, along with a similarly-dummied battle theme). Yasunori Mitsuda stated that the reason it was removed was because it was filler that affected the pace of the game. It was likely intended to be explored before the Tyranno Lair. Other removed locations include a Zeal dungeon and Robot Village in 2300 AD. Additionally, the Forest Ruins north of Medina were planned to be a full dungeon.
An old man (also seen in Masato Kato's initial sketches) was originally going to be a party member, and he apparently wielded a rod as a weapon.note This character is widely believed to be Gaspar in his Zeal clothing, who does not have artwork; however, a translation of the developer's comments shows that this is unspecified, and the kanji used to generically label him as an old man is different from Gaspar in the game. The character has a closer resemblance to Belthasar without a beard (which is also the case in the in-game sprites), and Melchior holds a staff that looks more like the concept art. It was such an early idea that it may have been any of the Gurus or even a predecessor.
The same set of character sketches that featured the old man also have a few other curiosities. Schala, for instance, originally bore an uncanny resemblance to Terra, and Lucca was originally named, of all things, Riddel.
According to Masato Kato, Crono's death would have been permanent; the party would instead recruit a version of Crono from the night before the Millennial Fair, and have to return him to his proper time during the ending, knowing that his fate is inevitable. This was scrapped because the other Square higher-ups thought it was too depressing.
Preview articles from magazines like V-Jump at the time can reveal some interesting development changes for the eagle-eyed:
At some point during development, the time Crono & co. lived in was going to look like a fusion of medieval Japan and Holland (with Japanese-style long houses and also windmills); none of these assets are anywhere in the game as shipped, but it does explain why Crono uses katanas (which is kind of inexplicable in the game as it shipped).
There was, at one point, an area with Zeal-like statues but that seemed to be made out of crystal.
The fields of the desolate future were going to be much more bleak at one point, with seething, magma-filled craters dotting the landscape. This is presumably the genesis of the crater enemies, who would've blended in much better to the backgrounds.
The Tyranno fight was, at one point, seemingly much different: the creature would walk out of the dark pen it's in rather than just be standing there with Azala (who is nowhere to be seen).
Gato (or a similar enemy) could actually be found in 65 million BC, but this may have just been a test enemy.
Similarly to Xenogears, this game was a scrapped concept for Final Fantasy VII that was spun off into its own game. That spin-off was further split into two games when it became clear the SNES CD add-on was a failure and cartridge memory would be an issue. Those games became Chrono Trigger and Secret of Mana. This could also explain why Crono/Randi and Marle/Primm share similar designs.
Johnny was planned to have a short boss fight before switching off to the racing seen in the game proper. He was also going to give himself the title of "The Blue Comet".
Other:
This was one of the last Square games to be developed on Apple hardware before they switched to Silicon Graphics workstations. Square is notable as one of few Japanese developers, if not the only one, to develop games on Apple computers, and at least one Square employee did all of his work on the Apple ][ well into the SNES days.
that the reason it was removed was because it was filler that affected the pace of the game. It was likely intended to be explored before the Tyranno Lair. Other removed locations include a Zeal dungeon