I had the same issue with my 2 official Wii U Pro controllers and found a fix. I changed the line below from =0 to =1 in the recalbox.conf under section D (controllers). After changing this and rebooting my Wii U controllers reconnect every time after a reboot or unplugged power to the recalbox.
controllers.bluetooth.ertm=1
THe problem is if i change this setting to "1" then my official ps3 controllers no longer reconnect automatically! I am using 2 Wii U pro controllers as my main 2 controllers and 2 ps3 controllers for when i want to play 4 players games.
So i have to choose whether i want my wii u controllers or ps3 controlelrs to reconnect to bluetooth after a reboot, i havent found a way to get both to work.
