@MichaelK About NES:
Please make sure that you have not done something wrong, there is supposedly no reason why this system has always been in last position, most likely you have made a wrong configuration (usually a typo, sometimes a space typed incorrectly: interferes and is not so easy to visualize ...).

See if this link helps you:
https://forum.recalbox.com/topic/22010/change-order-of-system-ports-not-working-rest-is-working-ok

The problem is finally solved - I bought a Trust YULA GXT 545 PS3/PC wireless controller with a dedicated dongle (set to D-input, buttons must be manually configured) for "Player 2" and everything works fine in RetroArch 🙂
Now the original PS3 controller (connected first on channel 1) works for "Player 1" and the game menu, and the Trust controller (connected second on channel 2) only works for "Player 2":
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@xtreemsurf Have you taken a look at the controls configuration menu? There you can set a controller for player 1, another for player 2, etc ...

Thank you very much, this solved my problem! I was changing things hundreds of times with no avail, luckily some laser-precise google search managed to find this blesses thread 😛

@luisvasquez That's something I sall do, one day or another ... At the very beginning of N64 autoconfiguration, pads assignement didn't work, that's players order is up to mupen for now

@haphzrd

the wiki contains share_init and not share.
You are in the wrong folder.

no,? what is the reason, that i add my XBOX Controller to Controller 1 and
in N64-Emulator is it Controller 2?

here under Controller Settings
https://github.com/recalbox/recalbox-os/blob/master/wiki/images/settings.jpg
is XBOX = 1
LOGITECH = 2

Edit
Found this
https://m.reddit.com/r/RetroPie/comments/4b5idq/change_controller_order/

Yes, done.