USB Loader GX attempts to only skip data you don't need, but on some occasions it actually skips data you do need. I would say that's the main reason. Generally it never skips anything that would be needed for playing the main game on the disc, though.
A second benefit of CleanRip is that it doesn't require you to install any cIOS on your Wii. So for someone who's new to Wii homebrew it's easier to set up, but if you already have cIOS installed then it doesn't make any difference.
A second benefit of CleanRip is that it doesn't require you to install any cIOS on your Wii. So for someone who's new to Wii homebrew it's easier to set up, but if you already have cIOS installed then it doesn't make any difference.