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parallel-n64
Optimized/rewritten Nintendo 64 emulator made specifically for Libretro. Originally based on Mupen64 Plus.
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There are also two texture packs that include improved models and such - I use DeathWrench's via Nerrel (also includes a remastered soundtrack) but Henriko Magnifico includes 4k textures so depends on what you want.
The thing is though, there's nothing that was stopping Nintendo to grab one of those emulators and use it themselves as most of them are open source, Sony actually uses an open source emulator on the playstation classic so the precedent is there, Nintendo could have taken one of those emulators and just improve on them: https://github.com/libretro/parallel-n64