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The jump to 3D was not kind for most games, a lot suffered from it. Some games, like Phoenix Wright, were able to make the transition successfully.
Pokemon was not one of them. GameFreak had a team of incredibly talented sprite artists, who were able to create extremely dynamic and emotion filled sprites, especially by the end of the DS era.
However, the jump to 3D was not kind to the Pokemon's visuals. The 3D models frequently used washed out and "safe" colors, always staying exactly on model with the official art. This has given the games a flat, boring look. Combining this with the poor animations, questionable poses, and inability to portray complex textures like fur, it's clear that there isn't a single 3D model that looks better than their predecessors.
Sprites can still work for a Pokemon game, and it's unfortunate that GameFreak will never return to them. Look at Octopath Traveler for an excellent example of this.
