Hi guys!
Finally I got the solution for that. What I did is to move from mupen64plus to libretro core (mupen64 but from libretro) under the N64 emulator settings to use.
Key mapping is now working as expected using Xbox One controller.
The problem about slowness (using libretro - mupen64) was caused because I already set libretro snes9x to use run ahead (latency settings) and saved the configuration, so N64 emulation was also trying to use run ahead settings that are quite bit processor intensive.
I just disabled run ahead (lantency settings) for this N64 core only, and now I am ready to go!
Thanks!