If you feel comfortable, you can fix it by editing your FFXIV.cfg file.

%UserProfile%\Documents\My Games\FINAL FANTASY XIV - A Realm Reborn

Find "<GamePad Settings>" and change the line beginning with Alias to:

Alias {90,91,88,89,41,40,32,33,73,72,48,49,3,2,1,0,4,6,10,5,7,11,9,13}

Save that file and then run FFXIV. All the mappings should be restored, but haptic feedback still isn's supported for some reason.