Im sure you've thought about this, but perhaps in the installer, check which OS we have and if we have an OS which allows for "one directory installing" to give us the option to utilize the Program Files / Application Data method (whatever it's actually called is beyond me atm). This way, if our OS supports it, we can choose for ourselves if we want to use it or not.
Ultimately, it shouldnt be TOO hard to keep track of the files no matter where they are for those of us who crank all over our OS's directories
