put this in i3config, instead of standard movement keys.
bindsym $mod+h exec "~/.config/i3/move-cursor.sh focus left"
bindsym $mod+j exec "~/.config/i3/move-cursor.sh focus down"
bindsym $mod+k exec "~/.config/i3/move-cursor.sh focus up"
bindsym $mod+l exec "~/.config/i3/move-cursor.sh focus right"
put this in ~/.config/i3/move-cursor.sh
#!/bin/sh
eval i3-msg $*
HERE=\xdotool getwindowfocus`
ULX=`xwininfo -id $HERE | grep " Absolute upper-left X:" | awk '{print $4}'`
ULY=`xwininfo -id $HERE | grep " Absolute upper-left Y:" | awk '{print $4}'`
if [ $ULX != "-1" -o $ULY != "-1" ]; then
eval `xdotool getwindowgeometry --shell $HERE`
NX=`expr $WIDTH / 2`
NY=`expr $HEIGHT / 2`
xdotool mousemove --window $WINDOW $NX $NY
fi`