Content Leak: Although the remake wasn't formally announced until E3 of 2017, the game's existence was expected since February of the same year due to a data mine that month revealing its name.
Short Run in Peru: The original game was released in North America first on November 17, 2003. It didn't come out in its native Japan until 4 days later with a metric ton of changes such as Trunkle healing itself if you attack its tree and healing for each object it inhales during said attack instead of just for a uniform 10.
The Other Darrin: The remake has Samantha Kelly and Kenny James doing Princess Peach and Bowser instead of reusing Jen Taylor and Scott Burns' voice clips.
Starbeans Cafe was originally intended to have cameos from other Nintendo games — such as Samus from Metroid and Link from The Legend of Zelda — when you create new drinks, but they were dropped and replaced by the various appearances of Professor E. Gadd.
BP-restoring items were originally baked goods, rather than the syrups used in earlier Mario RPGs and the final game.
The brothers were originally allowed to use either jumping or hammers to dodge and counter attacks, with jumping on the face buttons and hammers on the shoulder buttons. The final game, and subsequently the rest of the series, has jump/hammer counters pre-determined for enemy attacks.
Dying worked more like traditional role-playing games in the prototype: when a brother ran out of health, he'd do a Death Throws animation and land on top of his status icon, and when revived he'd return to the battle on a platform a la Mario Bros.. In the final game, he collapses on the ground and the surviving brother has to carry him when dodging enemy attacks.
A hooded Beanish character whose sprite was Dummied Out of the final game has a quest in Beanbean Castle Town, where the brothers have to navigate the town and talk to several NPCs while it's pitch-black.
The Yoshi-based section of the Beanstar quest was framed differently. The Yoshi Theatre doesn't exist, and instead of collecting Bean Fruits to feed to several Yoshis, a single Yoshi needs to be fed several "cultivated mushrooms" so it can retrieve the Beanstar piece from across a lake. The general design of the quest remains the same, as does Piranha Bean. Additionally, all the Beanstar pieces looked like mini-Beanstars rather than individual chunks of it.
An NPC in Beanbean Castle Town reveals that Cackletta is Queen Bean's jealous younger sister.
Bowletta's design is vastly different, and essentially inverted in concept: the prototype design is a gruff, bulldog-like version of Bowser with Cackletta's mannerisms, while the final design is moreso Cackletta's face on Bowser's body.
Bink was alive and thus looked even more like Donkey Kong, instead of being a skeleton like the rest of the S.S. Chuckola crew.
Why Fandom Can't Have Nice Things: After an American reviewer leaked the 3DS remake online, Nintendo of America has decided to crack down on who gets review copies and when. This means that there will be a significant decrease in reviews before their future game releases.
Other Trivia:
The original Superstar Saga is one of the few Game Boy Advance games with special features when played on the Nintendo GameCube's Game Boy Player. The game is programmed to use the rumble function and allows a second controller to be plugged in and used at the same time as the player 1 controller.
◊. This was fixed in the 3DS remake.
