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>Gen 1
Suffers from a lot of repetition. Lines such as Poliwag, Diglett, Doduo, Magnemite and Voltorb have very simplistic evolutions with little to no change in appearance and aesthetic but this in no means makes them bad designs except possibly Poliwrath and Magneton.
>Gen 2
It continues the simplicity of design introduced from Gen 1 as well as expands some evolutionary lines from gen 1. A number of great designs. Not a single overall bad design in my opinion.
>Gen 3
Pokemon ditches simplicity and begins getting detailed and eye catching. No pokemon is offensively bad except possibly Blaziken who I feel has a good design but there are an incredible number of forgettable pokemon.
>Gen 4
Flashy and cool remains the look but now there are some questionable designs thrown in such as Drapion and Kricketune. The abundance of expanded evolutionary lines is a real hit and miss. Weavile, Roserade, Porygon Z, and Porbopass (fight me) are the better of them. Worst offenders are Rhypherior, Lickilicky and Ambipom. The main legendaries and Arceus are incredibly overdesigned compared to previous ones but it fits them. The Lake Trio however look incredibly boring and samey.
>Gen 5
They got pretty bold with the patterns and flashiness and even decided to emulate Gen 1 pokemon. The starters are regal and proud looking but Emboar is all over the place. Samurott gets a lot of slack but I like his design. The Elemental Monkey evos, the Klink line, and the Cubchoo line are just bad and mons like Alomomola are incredibly forgetable. The legendaries look very out of place except vanilla Kyurem and the genies are just awful. Keldeo is probably the ugliest shit in all regions and Cobalion is the only garbage musketeer. Everything else is fine.
>Gen 6
Very small and rather unimpressive save for some gems. Worst starter designs and 3D models did not help. Diggersby, Aromatisse, the Pyroar line and Goodra are just awful. The legendaries aren't bad but Hoopa is literally who.