Let's travel back in time all the way to the release of Metroid Prime Trilogy. Pretend that you are Nintendo, only smarter. You see that MPT will not load properly on any known softmod, but there is a workaround that will bypass the main menu and skip directly to the games, with the use of the alt .dol method. Remember, you are smarter than the real Nintendo, so you take your next big launch title, New Super Mario Bros. and you set it up to where the game must load different .dols to run properly. Instead of running the options and gamesaves in main.dol and everything else in some other .dol, you run the menu and the overworld map on main.dol and the levels in individual .dols (world1-1.dol, world1-2.dol, world1-3.dol ...) This would be playable one level at a time, but would ruin the experience of the game to the point that only 5 of the one jillion people playing this game are using a backup method.
Could this be cracked? Maybe. It might have to be cracked on a per game basis, though and we wouldn't have games like New Super Mario Bros. days before the official release like we do now. I don't have the first clue as to a proper fix to the problem but perhaps right now someone smarter than me can come up with a solution before a game comes along that won't run at all without .dol reloading.
Could this be cracked? Maybe. It might have to be cracked on a per game basis, though and we wouldn't have games like New Super Mario Bros. days before the official release like we do now. I don't have the first clue as to a proper fix to the problem but perhaps right now someone smarter than me can come up with a solution before a game comes along that won't run at all without .dol reloading.