I've noticed that when working on creating a game, that I have a bunch of mods that I want to keep updated to latest, but that I also want to tweak their textures to create a unified style for the game. Unfortunately, it seems like the only way to modify the textures in the game itself is to change the textures in the mod folders and then to keep re-applying the textures to the mods every time the mods are upgraded. I assumed I could just create a texture folder in the games folder and dump custom textures in there that would override all the Mod's textures, kind of like we do now for texture packs. Unfortunately this didn't work. I think it would make sense for texture packs in the normal textures folder to work as they do now, overriding game textures.
What I'm saying is that any texture in games\[gamename]\textures should automatically override all the game's mod textures. This shouldn't be configurable by the player. If they want to modify the games texture, they should enable a texture pack the way they normally do.