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I've always determined a Pokemon design's quality by how easily I could imagine it living in the wild, or whatever setting the story assigns it. Not OUR wild, obviously. The Pokemon world is pretty fleshed out and it's easy to suspend your disbelief, up to a point.
Almost every Pokemon in Gen 1 and Gen 2 are easily believed to live in that world, though there are obvious exceptions.
Pokemon like Mr Mime, Jynx, and Voltorb/Electrode don't really work in the wild. I can't think of any setting they'd fit at all and I consider those to be poor designs.
Meanwhile, Grimer/Muk could easily exist in heavily polluted areas, and Growlithe/Arcanine are just wild dogs.
Porygon is purely computer code given form and doesn't live in the wild, but this is explained by the story and easily justified in the low key "high-tech" setting. The fact that you can't encounter it in the wild helps to support its plausibility.
Pokemon like Magnemite/Magneton are a bit harder to justify or dismiss. Given the world they're in, it's not impossible to assume magnetic forces could combine to create life, but it's in a bit of a grey area for me. They've always seemed out of place, but not overly fantastical for the setting.
Ditto is pretty similar. In Gen 1 you could only find it in the basement of an abandoned lab with references to DNA research, which totally works. You can pretty easily assume it's a failed experiment.
But in Gen 2 it's just out in the wild, conveniently by the Day Care and nowhere near the laboratory. Much harder to justify.
People criticize Gen 2 designs as being overly simple, but I think that helps a lot. It's easy to imagine a Furret or Magcargo living in the wild (although not on fucking Cycling Road, Game Freak).
