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Low quality models, animations, and special effects, even at the time. Most, if not all, the Pokemon models for the first 251 were directly ported from Stadium 1 and 2. Since X/Y, Game Freak has been using the same models, maybe with a few touch ups here and there, to save them the effort of redoing all 800+ Pokemon every generation. These models are high quality, intended to last them a long while, but the 3DS resolution isn't great so they look a lot shoddier than they actually are, and the 3DS's rendering is subpar enough to cause slowdowns when there are multiple of these models on screen. It's really more the 3DS's fault if for being underpowered than Game Freak's laziness. The best solution for performance would be to make models with less polygons for scenes with more than 2 Pokemon, to keep the framerate steady.