With a few modifications to the remap and input from @somiatruites, @flaker38 and documentation from @Atari finally I found a quite good config.
First of all the gamepad should be connected as Xinput (to swap gamepad mode just press Start + B Button for 5 seconds). Batocera will show a contextual box with the gamepad connected.
this is my Mupen64Plus-Next.rmp, located at /share/system/.config/retroarch/config/remaps/Mupen64Plus-Next
input_libretro_device_p1 = "1"
input_libretro_device_p10 = "1"
input_libretro_device_p11 = "1"
input_libretro_device_p12 = "1"
input_libretro_device_p13 = "1"
input_libretro_device_p14 = "1"
input_libretro_device_p15 = "1"
input_libretro_device_p16 = "1"
input_libretro_device_p2 = "1"
input_libretro_device_p3 = "1"
input_libretro_device_p4 = "1"
input_libretro_device_p5 = "1"
input_libretro_device_p6 = "1"
input_libretro_device_p7 = "1"
input_libretro_device_p8 = "1"
input_libretro_device_p9 = "1"
input_player10_analog_dpad_mode = "0"
input_player11_analog_dpad_mode = "0"
input_player12_analog_dpad_mode = "0"
input_player13_analog_dpad_mode = "0"
input_player14_analog_dpad_mode = "0"
input_player15_analog_dpad_mode = "0"
input_player16_analog_dpad_mode = "0"
input_player1_analog_dpad_mode = "0"
input_player1_btn_a = "0"
input_player1_btn_b = "1"
input_player1_btn_r2 = "20"
input_player1_btn_select = "22"
input_player1_btn_x = "23"
input_player1_btn_y = "21"
input_player2_analog_dpad_mode = "0"
input_player3_analog_dpad_mode = "0"
input_player4_analog_dpad_mode = "0"
input_player5_analog_dpad_mode = "0"
input_player6_analog_dpad_mode = "0"
input_player7_analog_dpad_mode = "0"
input_player8_analog_dpad_mode = "0"
input_player9_analog_dpad_mode = "0"
input_remap_port_p1 = "0"
input_remap_port_p10 = "9"
input_remap_port_p11 = "10"
input_remap_port_p12 = "11"
input_remap_port_p13 = "12"
input_remap_port_p14 = "13"
input_remap_port_p15 = "14"
input_remap_port_p16 = "15"
input_remap_port_p2 = "1"
input_remap_port_p3 = "2"
input_remap_port_p4 = "3"
input_remap_port_p5 = "4"
input_remap_port_p6 = "5"
input_remap_port_p7 = "6"
input_remap_port_p8 = "7"
input_remap_port_p9 = "8"
And this is my es_input.cfg located at /share/system/configs/emulationstation
<inputConfig type=“joystick” deviceName=“Microsoft X-Box 360 pad” deviceGUID=“030000005e0400008e02000072050000”>
<input name="a" type="button" id="2" value="1" code="307" />
<input name="b" type="button" id="0" value="1" code="304" />
<input name="down" type="hat" id="0" value="4" />
<input name="hotkey" type="button" id="8" value="1" code="316" />
<input name="joystick1left" type="axis" id="0" value="-1" code="0" />
<input name="joystick1up" type="axis" id="1" value="-1" code="1" />
<input name="l2" type="button" id="4" value="1" code="310" />
<input name="l3" type="button" id="10" value="1" code="318" />
<input name="left" type="hat" id="0" value="8" />
<input name="pagedown" type="button" id="5" value="1" code="311" />
<input name="pageup" type="axis" id="2" value="1" code="2" />
<input name="r3" type="button" id="9" value="1" code="317" />
<input name="right" type="hat" id="0" value="2" />
<input name="select" type="button" id="6" value="1" code="314" />
<input name="start" type="button" id="7" value="1" code="315" />
<input name="up" type="hat" id="0" value="1" />
<input name="x" type="button" id="3" value="1" code="308" />
<input name="y" type="button" id="1" value="1" code="305" />
</inputConfig>
With this config we have the next in:
Emulation Station
A Button to confirm
C Down to go back
On Retroarch emulator

Home + A Button -> open Retroarch menu
Home + C Down -> restart emulator
Home + Start -> exit Retroarch
Home + D-Pad Up -> go to next save state slot
Home + D-Pad Down -> go to previous save state slot
Home + C Left -> load State
Home + B Button -> save state
Home + ZL -> screenshot
Home + Start -> return to ES menu
Hope this could help others to get this incredible gamepad up and running.
I focused to get the config for Retroarch (I really like Retroachievements 😝)
I want to thanks to @somiatruites, @flaker38 and @Atari!!! (I just played with your guides, documentation and config files to get it work)