When I load the game (super mario bros) it appears that controller input is disabled, but if I wait about 90 seconds it starts working!!

I have the exact same problem, but I haven’t even configured emulator specific controls (yet). Just did the first time config and then edited it a bit. I’m using RetroPie 3.0 and Wii Classic pad with Mayflash adapter. Works like a charm, but the delay is really weird AND annoying and sometimes totally random length. :( It also feels like pressing some buttons can activate the controller faster, but I’m not 100% sure about that, I’ll have to experiment more.