FunkiiU doesn't have a GUI and has annoying command system but it works under Linux and Mac OSX devices.
Wii U USB Helper has GUI, no need for commands, works under Windows and Android. You can also download 3DS games with it [3DS section still thinks that it only downloads Wii U games, wut]
Basically FunkiiU for Linux and if you want to make your life extreme [Ex. New game gets uploaded to database, you can grab it using FunkiiU but it will be unusable until .tik is leaked]