Replacing textures in the ISO is technically doable (though you might need a game-specific tool for it). The problem with it is that the game might not be able to handle high-res textures properly, and it's more cumbersome, so I don't think anyone does that.
You could try to use the following PR build and enable the "Prefetch Custom Textures" option. It uses a lot of RAM and makes it take a bit longer to start the game, but once the game is running, texture loading will be fast. The option will hopefully be available in the regular development builds at some point. http://dl.dolphin-emu.org/prs/pr-2162-dolphin-latest-x64.7z
You could try to use the following PR build and enable the "Prefetch Custom Textures" option. It uses a lot of RAM and makes it take a bit longer to start the game, but once the game is running, texture loading will be fast. The option will hopefully be available in the regular development builds at some point. http://dl.dolphin-emu.org/prs/pr-2162-dolphin-latest-x64.7z