Framerate dropped somewhere at 30-45FPS on o3DS and 2DS. N3DS got 40-50FPS. Remember that Sun and Moon have 3GB and I'm sure that unused models like 801 pokemon overworld models(minus the numbers of pokemon that are found in the overworld like your starter in the beginning or Mimikyu) might be the cause of the lag. That's the reason why GF removed the 3D Mode.wait the acual 3ds cant get 60fps on royal?
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For Citra, it can break that point with your processor and Graphic Card.
On my video, a simple sped up would make a 60FPS video like KazoWAR or Shofu.