Copypasta from the first post
"EASY WAY (TESTED) (Credit to dfgas)
1) Insert the Disc and launch NeoGamma R6/USB Loader and launch game without alt. dol but with the 002 fix on and create a save file
2) Turn the 002 Fix and alt. dol on and select the .dol from discs, if you want to play a game, you select its .dol so:
a) rs5mp1_p.dol = Metroid Prime 1
b) rs5mp2_p.dol = Metroid Prime 2
c) rs5mp3_p.dol = Metroid Prime 3
3) Select the .dol for the game you want to play, the game will launch directly and will not load the trilogy menu."