So I happened upon this in the google code site for genplusgx, while there is no new download in the Downloads section. Under the Issues section there was a request to add Wii U Pro Controller support, and I happened upon it yesterday, and the creator, ekeeke was troubleshooting just as I happened to be looking, and he uploaded a version that seemingly allowed for Wii U Pro controller support, though it seemed that it might not be perfect (and its not the Wii U Pro controller auto syncs to player two, fortunately you can change the player 1 input to the player 2 classic controller which works as the Wii U Pro controller. You still have to navigate with the Wiimote to load the game and options though. Anyway, the issue has been taken down, and so too has the download. But I happened to download it, and I've uploaded it here. Keep in mind that this is not official, and ekeeke, if you see this and don't want me posting this, let me know and I'll take it down.
http://www.mediafire.com/download/sded9x9a4kmb05f/boot.dol
http://www.mediafire.com/download/sded9x9a4kmb05f/boot.dol