For us USB Loading fools, I've been exploring how to play this game properly off the HDD.
The game comes with 5 .dol (executable) files.
main.dol (default) = select/create your save, set options & configure settings (shared by all 3 games), check/exchange vouchers (for all 3 games), check/unlock extras (for all 3 games). Electing to launch the single player or MP2E multiplayer modes reboots the Wii. By loading main.dol, the game requires a (any) disc in the drive to work. If that issue was ever overcome via Cfg USB Loader, I'd love to learn how...
rs5fe_p.dol = seems to be identical to loading main.dol. I imagine that the "fe" stands for front end, but if the front end requires a separate dol reload, I don't understand how loading main.dol even worked...
rs5mp1_p.dol = Metroid Prime. Loads straight into the game, presumably using the previously set up/selected save file. Skips straight to introduction. No disc required in drive. Perhaps a menu's missing? I didn't see any way to change the difficulty level... and some of my settings didn't persist.
rs5mp2_p.dol = Metroid Prime 2: Echoes. Loads straight into the game, presumably using the previously set up/selected save file. Skips straight to introduction. No disc required in drive. Perhaps a menu's missing? I didn't see any way to change the difficulty level... and some of my settings didn't persist.
rs5mp3_p.dol = Metroid Prime 3: Corruption. Loads straight into the game, presumably using the previously set up/selected save file. Skips straight to introduction. No disc required in drive. Perhaps a menu's missing? I didn't see any way to change the difficulty level... and some of my settings didn't persist.
After playing MP1 up to the first save spot, I see why the settings didn't persist. Reloading main.dol shows me that progress was saved into slot 1, which is now some form of half-created slot. It shows that I'm 0% and 14 minutes into a Veteran MP1 run, but shows no Mii in the Mii slot. Woops. Trying to select this borked slot results in an error message stating that the Mii associated with this file (there wasn't one, since I had set up slot 3 as my preferred slot) has been deleted, and that a new Mii must be selected. I deleted slot 3 and reused my preferred Mii, and now things seem to be working correctly.
The alternative dol trick seems to mostly work, as we can access all 3 campaigns (but seemingly, only 1 of the 3 save slots); but it looks like some game-specific menus might not be available this way, or the MP2E multiplayer mode. I'll continue playing around with this later tonight, and compare it to the straight up legit disc-load method the game expects of us.
Edit - Ok, loading from the disc, I don't see any menus that I wouldn't normally have access too. It looks like if you try to load a new single player campaign for any of the 3 games from the usual menu, you'll be able to select your difficulty level there. Of course, the game will reset instead of continuing. But you can then use the alternative .dol trick to load straight into the core MP game you're were trying to run. Settings should persist if you stick with save slot 1. Still can't figure out a way to load the multiplayer.