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I used to not care for a lot of Hoenn Pokemon, but after seeing them in later games, I realized that it wasn't the designs themselves that bugged me, but rather their sprites. For example, when I play the story modes I pick mons based off designs, so when I went through Gen 3 I went with Pikachu for my electric mon because I didn't like Manectric's design. However, when I did a mono-electric run of Volt White, I took a second look at Manectric and found him to be much more visually appealing, so he earned a spot in my party, and is now one of my favorite Gen 3 mons.
Something just seems...off about Gen 3 sprites. I can't put my finger on it; maybe someone more artistically inclined can point it out? Or maybe I'm just crazy?