Hey Daidara, I'm a bit new to the forums myself, but you may find the page for Metroid Prime on the Dolphin Emulator Wiki helpful;
https://wiki.dolphin-emu.org/index.php?title=Metroid_Prime_%28GC%29
There are known issues with Micro-Stutter, savestates, your visor in-game, and more, however, it doesn't seem to require any non-default settings to run properly. Just take a gander over on that page and see if this help you solve any of your lag issues.
I would also make sure you at least try the latest Development version (it doesn't have to replace your current one, the Stable version, from what I understand you're using):
https://dolphin-emu.org/download/
It would be version 4.0-5762.
https://wiki.dolphin-emu.org/index.php?title=Metroid_Prime_%28GC%29
There are known issues with Micro-Stutter, savestates, your visor in-game, and more, however, it doesn't seem to require any non-default settings to run properly. Just take a gander over on that page and see if this help you solve any of your lag issues.
I would also make sure you at least try the latest Development version (it doesn't have to replace your current one, the Stable version, from what I understand you're using):
https://dolphin-emu.org/download/
It would be version 4.0-5762.