Because if you patch your game the hard way, you can't play on AltWFC server anymore?
Because users prefer keeping a clean ISO for future use in case of patch update/etc?
Because it's easier to set an option in the loader instead of patching an ISO for users who don't understand how folder and files are working on a computer (and trust me, there are a LOOOT who don't)
Loaders and patcher are doing the exact same thing! it replaces https://nintendowifi.net -> http://wiimmfi.de
So why use the hard patch when the loader is doing it the same thing without the burden to edit the iso on computer?
The only exception is for Mario kart, the loaders don't patch the match-encounter algo, but it doesn't prevent users from playing online and finding random players.
The match-making algorithm patch only removes restrictions on player's level (which isn't better to keep for noob like me, who never played in 100cc or more than 10 times online?) and region restriction if I remember well.
Ah, the Mario kart patcher is also editing displayed text on error messages. not really required/useful.
I guess I can see your point. I'd rather see just one custom server service and that should be Wiimmfi. IMO it's silly to have two teams when all efforts should be focused on making one awesome service.