Version Differences

Prime

There are a ton of version differences for Metroid Prime, so check out this link from The Cutting Room Floor: https://tcrf.net/Metroid_Prime/Version_Differences

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.