I Edited /etc/emulationstation and replaced the code with this..

#!/bin/bash

es_bin="/opt/retropie/supplementary/emulationstation/emulationstation"

if [[ $(id -u) -eq 0 ]]; then
    echo "emulationstation should not be run as root. If you used 'sudo emulationstation' please run without sudo."
    exit 1
fi

if [[ -n "$(pidof X)" ]]; then
    echo "X is running. Please shut down X in order to mitigate problems with loosing keyboard input. For example, logout from LXDE."
    exit 1
fi

key=""

x=0

echo "Waiting up to 60 seconds for Joypad 1"
while [ "$x" -lt 60 -a ! -e /dev/input/js0 ]; do
   x=$((x+1))
   sleep 1
done
if [ -e /dev/input/js0 ]
then
   x=0
   echo "Joypad 1 Enabled :) Waiting up to 10 seconds for Joypad 2"
   while [ "$x" -lt 10 -a ! -e /dev/input/js1 ]; do
      x=$((x+1))
      sleep 1
   done
   if [ -e /dev/input/js1 ]
   then
       echo "Joypad 2 Enabled! Starting Emulationstation"
       $es_bin "$@"
   else
       echo "Joypad 2 not found"
       $es_bin "$@"
   fi
else
   echo "Joypad 1 not found within time limit; Aborting!"
fi

This makes retropie pause for up to 60 seconds for me to turn on my controller. If I don’t do it, it quits back to the bash prompt (if I don’t turn on a controller I probably don’t want to play games, I want to work on the config), if I do turn on a controller it waits up to a further 10 seconds for me to turn on a second controller, whether I turn a second controller on or not it will then start ES.

If I have finished playing with configs and just want to go into ES now, I can just type ‘exit’ and ES runs.

This could be improved to do something similar for 4 controllers and even make the “Turn on controller now” message a bit clearer. It comes up after the splash screen closes but isn’t clear from 10 feet away