Version Differences

Prime

Performing a Dash Jump off scan points is only possible in the 0-00 NTSC release.
The Aboretum Gate Jump is not possible in any version except the original 0-00 NTSC release.
The Area Voice in the European and Japanese release differ. In the Japanese release, the Japanese names of all of the areas in the game are spoken when loading a save game, and ONLY when loading a save game. In the European release, "Tallon Overworld" and "Impact Crater" are spoken when traveling to each, respectively.
The Artifact of Warrior will disappear if you leave the room in the 0-00 and 0-01 versions. This is avoided in the 0-02 version by placing a lock on both doors until collected. While in the European and Japanese release, the artifact will not disappear.
Baby Sheegoths have double life in Japanese, European, and Australian releases.
The door behind the Bendezium rubble in Central Dynamo is locked in every version except the 0-00 version.
The door leading to the Plasma Beam in Geothermal Core is blocked on all versions except 0-0 and 0-01 NTSC. In Japanese/PAL versions, a pile of Bendezium lies in front of the door, requiring a Power Bomb to destroy. In 0-02 releases (also known as Player's Choice), the door is locked until Grapple Beam is obtained.

The size of the screw attack is bigger in Trilogy so that it isn´t possible anymore to go out of bounds through Morph Ball tunnels.
Spider Guardian´s damage inflicting barrier was shortened in Trilogy so he can´t hit you through walls anymore.
Ing Smashers in Hall of Combat Mastery will lock the door the 1st time they appear in Trilogy.
The Jump Guardian Trick was removed in the Trilogy and Japanese GC Version.
The Portal Shortcut in Agon where you only needed to destroy the 1st and the 3rd lens was altered in the Japanese and Trilogy version which means that you need to destroy the second one too to activate the portal.
In the NTSC GC Version it was possible to Slope Jump on a wasp nest left to the half-pipe that leads to seeker to get it earlier without Boost Ball. It was removed in all other versions.
In the NTSC GC Version there is an Ing Pod that is positioned near the Save Station that let´s you Space Jump up to the 3rd Temple Key in Torvus so that you don´t need Grapple for it. It was removed in every other version.