@rbezares I had this a couple of days back, somehow es had managed to remove it self, I refreshed the card and it happened again, although got slightly further in the boot as es did appear before crashing. I flashed a new image to a different micros and it has worked fine since so am putting it down to a bad card
Did you configure the controller via Emulation Station correctly? Maybe do it again to be sure.
There's a script to assign controllers to players. It works very well for me. Maybe it's worth a try for you.