Textures look awesome, but there should be a better way to install them, without replacing existing files.
For the CORE textures, you just copy the folders there. Nothing gets copied over. And, if you don't like a specific graphic, you just go in and delete them.
As for the mod textures ... that's how they are setup. But, if you don't like a specific mods textures - you can always just delete the mod, and just re-download it. Or, copy the mod folder (in your "mods" directory), add the textures into the copied mod folder, then change the title in the About.xml of that copied mod (so you can differentiate the two).