I'd like to know a way to separate some space on my hard drive for the Wii U, you know, for installing games and such, but still have the rest for general usage. I believe the Xbox 360 had some thing similar, and wonder if it would be possible to do it here, either though my PC or some homebrew application on the console itself.
The problem is the Wii U sees any partitioned drive as not in Wii U format and asks to format it.
Technically you can use FAT32 for Wii U games/saves by using Mocha, so you only need one FAT32 partition on the HDD that can contain both Wii U and vWii content. But there are a few caveats:
1. R/W speeds are very slow on FAT32, it seems to be an issue with the Wii U's FAT32 driver, as SD cards have the same problem when using Loadiine.
2. You can't install games by the normal method. The ticket needs to be installed to the Wii U and the game data needs to be manually moved onto the HDD. You can't install just the ticket, so the easiest (but slowest) method would be to install the game to the internal memory, and manually move the whole thing to HDD with wupserver. Once installed the games work fine (besides long load times), so this only needs to be done once per game.
I heard if you install a DLC or update for the game to internal memory first, then you don't need to install the full game, you can simply move the game (in Loadiine format) from your PC onto the USB after installing the DLC or update. I've only seen this mentioned in one thread though and can't confirm whether it works. That way you don't need space on the internal memory to install it there first, plus it speeds up the install process a lot, since the whole game can be copied from your PC onto the USB in minutes. This method may be better than the one mentioned above.
The FAT32 method is really not recommended for Zelda BotW because long times there are excruciating on FAT32, they can be 15 minutes long and every time you enter/exit a shrine or teleport you get another loading screen...
But on a 32GB Wii U you could put BotW on the internal memory along with the other main culprits for long load times (there are a few of them, notably Super Mario 3D World and Pokken Tournament, and I think maybe Twilight Princess HD, but most games actually have reasonable load times on FAT32), and have the rest on a FAT32 HDD, if you don't mind going through the slow/somewhat complicated install process for each game.
Some people use the SD card for vWii and have a HDD dedicated to Wii U, that seems to be the best option for load times. A 128GB SD card should fit most of the Wii games you would want, and 200GB should be plenty. But Wii games will only load from SD with WiiFlow or CFG Loader, not USB Loader GX. Wii/GC games will load slower from the SD card but that's not really an issue as the DVD drive in the GC/Wii was pretty slow anyway, we've just gotten used to faster load times with USB.
You may have issues with GC games that use streaming audio (only a handful do), or games that have a lot of FMV cutscenes, that's just a guess though. But mostly GC/Wii games should be fine loading from SD.
There wasn't an other way to answer, unless you want to write 500 word paragraph why.
Not application but a true CFW would help. (It's system restricted)
This is how to make a proper answer