I just want to start my Miiverse account over, but to do so, I have to transfer the NNID to another device(my brothers 3ds). He has to have his system reformatted for that to work. When he got the 3ds, Mario 3D Land was already downloaded, and he has 3 years of progress on it. I can't delete my own NNID because mine is also linked to our WiiU, which has splatoon on it, and if I delete my ID, there goes my progress. Is there any way to keep his progress (or mine?)?
Your brother got a 3DS with a preinstalled game, that means at that point when he created a Nintendo ID the game was linked to his Account which means he will loose the game and its progress if you delete his NNID.
This is the Problem of the NNID and the 3DS, you cannot switch a NNID unless you do a factory reset which again ends in deleting the NNID and loosing games and progress. I also found no possibility to just unlink your NNID from your 3DS system.
Just to warn you, you can only delete his NNID to link another id to the 3DS device, but he will loose every game and progress and even purchases he made in the e-shop.