Microsoft came up with it, BTW, and all Mojang did was to follow the standard set by MS, and following the target OS' standards is generally one of the best programming habits to develop. As I understand it, the only problem caused by not following the standard occurs if you use non-standard Unicode characters in your folder names.
You don't need a great deal of knowledge to use APPDATA... Since it's under your personal home directory you automatically get all access privileges by default and everyone else is blocked except the Administrator account (if you've activated and password protected it). This is the primary reason APPDATA exists anyway... All of your system customizations live there, by the way, such as your Outlook mail databases (if you use Outlook), "favorites" folder if you use IE, etc.
All you need is enough "Search Fu" to google it on line or enough curiosity/interest to buy one of the many books describing the environment of the Windows version you use.
I have never seen any other programs install themselves in APPDATA like Minecraft did. Never ever seen it, not once, not a single program I've ever installed. But yeah, we can blame Microsoft, I'm fine with that if it's their "standard".