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Being conceptually good doesn't mean shit if it's not good in execution, though. A lot of my favorite gen 1 pokemon are literally just real life animals at a conceptual level, but their fantastic and memorable designs sell them. Sandshrew, Rhyhorn, Kingler, Cloyster; all superb designs. The gen 1 designs were mostly very simple and basic, there was nothing super clever going on and I don't think there needed to be.
Conceptually I guess I'd say Parasect is the most interesting, what with the fungus taking over the pokemon and zombifying it. Porygon is a good pick too, and I also think Cubone is neat. I think there's a lot of later gen pokemon that are conceptually really interesting but just come out of the oven looking fucking goofy, and if it doesn't have a memorable visual design I can't consider it a well designed pokemon.