they generally have some protections in place to prevent people from running unauthorized code on the system, though. not something I know anything about but I do know at the very least it's possible to burn a game to a disc and run it on a homebrew Wii.
actually backporting Prime 2 maps into Prime 1 is on my to-do list sometime soon since I think it would be fun. because yeah, the two games are very very similar internally.
Retro has basically completely changed everything twice... once for MP3 and once for DKCTF. so MP1 and MP2 are very similar, as are MP3 and DKCR (surprisingly enough).
I dream about the possibility to to link each metroid prime game by their starting point from samus space ship instead of connecting the maps between them. You could conserve your stats and item and go and come back between the games at anytime.
I know companies like datel (freeloader) have unofficially mastered discs that are runnable in an unmodified GameCube..
However, they have access to very sophisticated replication equipment and the means to forge a GCN filesystem, GCN sector-layout (basically standard DVD-ROM written from outside edge of disc inward, with a simple XOR-based cipher), and the disc's BCA (which can't be made with a DVD-burner).
Realistically speaking, your best bet at playing a custom GameCube disc is by installing a drive-chip or something to play DVD-Rs