In an interview with The Lost Levels Phil Sandhop, EarthBound Zero's English script writer, described the process of turning MOTHER into the final build of Earth Bound:

As a general rule with games produced by NCL, the development teams continue to work and tweak their projects that they know will be localized and produced in other territories. Often they will address their own desires that were not completed due to time constraints or not completed to their satisfaction and they will also address issues raised by Japanese consumers as that release hits the street.

American consumers are often very vocal about the length of time this process takes, but they really do get a much better product than they would otherwise.

In software development, each subsequent version is usually derivative of prior versions. Once the program was changed they would have continued to use the revised program and plugged in their old text modules.

The changes the development team continued to make after the Japanese release of MOTHER were rolled into the version of Earth Bound that was completed, but never released, in 1990. But they wouldn't be seen by Japanese audiences—wouldn't even be released officially—until 2004, when the definitive version of MOTHER was finally released on Game Boy Advance.

• The screen animates when you learn a melody. The original release of MOTHER lacked Earth Bound's brief light show.
• The order in which Ninten and Ana learn PSI is different
• There's a run button! Earth Bound's run button was originally for the debuggers and play-testers, and was kept at Phil Sandhop's insistence. In MOTHER 1+2 it was a planned feature all along, so the rest of the world doesn't try to keep up.
• There's no "Map" item. In the original version of MOTHER the map is yet another item that takes up space in Ninten's tiny inventory; in Earth Bound and MOTHER 1+2 the developers were kind enough to leave it out, although they didn't think to give him a cute yellow backpack.
• The CHECK command gives you a one-line description of each enemy. All of those one-line enemy descriptions (the doll "stares back at you") were written for the English release, and appear here in Japanese for the first time.
• The strip club is no longer a strip club, the crows have given up smoking, and the Gang Zombies have put their ties back on. In his interview Phil Sandhop says that all the censoring was done by Nintendo of Japan, and the graphics used for MOTHER 1+2 reflect that.
• The Repel Ring is in, the Friendship Ring is out. In the Famicom version of MOTHER a girl in Magicant gave you an item called the Friendship Ring. Whatever it did, it probably wasn't as useful as the Repel Ring, which staves off the game's innumerable random encounters for a few steps.
• The Crystal Caverns and Rosemary Manor are considerably simpler. In an attempt to smooth out MOTHER's notoriously strange spikes in difficulty, these two dungeons were simplified for the American release. In MOTHER 1+2 the simpler versions remain.
• The Old Man of the Fountain in Magicant acts as an ATM. What a guy!
• Enemies appear in the train tunnels. In an attempt to make MOTHER a little harder to play out of sequence, the train tunnels in Earth Bound were filled with tough enemies to keep you from passing through. They're still there in MOTHER 1+2.
• The Healer restores your HP What a guy!
• The endgame is completely different! In MOTHER's truncated ending you were warped to Magicant automatically after getting EVE's melody; in Earth Bound (and MOTHER 1+2) the ending is longer, and it begins by making you go there yourself. Other parts of the game are affected, too—the Philosopher's song is a version of the English translation, to take into account the XX Stone giving you the final melody.
• The ending is completely different! The epilogue, both the music and the text, was original to Earth Bound and appears in MOTHER for the first time here.