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Gens 3 & 4 tie for first.
These were the perfect balance between complexity and simplicity with the majority of the range looking very good, iconic, interesting, and straight up cool. Their respect mascots, Groudon, Kyogre, Rayquaza, Palkia, Dialga, Giratina, and the lauded Arceus are all incredibly iconic fan favorites that also strike perfect balances. Not to mention Excellent additions like Deoxys and Darkrai who are highly coveted just for how cool and rare they are.
Gen 1 gets second.
While some gen 1 designs are a bit wonky like Magneton, dugtrio, and Dudrio who are just "the same but an addition head or a few put together" or Muk which is just a bigger Grimer, The vast majority of the designs are simply iconic and soulful to the extreme and are very recognizable and elegant in their simplicity.
Gen 5 takes third place
Gen 5 has a lot of really good designs that very much feel like badass monsters. A lot of the designs are very well thought out and lack the addition of random and unnecessary additions to flesh them out like stripes or spikes that don't need to be there found in later gens. However despite how cool and fleshed out some of the designs are this gen began the trend of more ridiculous, silly, and inanimate designs that would be exasborate in later generations with the infamous Ice cream and trash bad pokemon. It's peaks are very high, and there are a lot that reach that peak in it's range. Victini, Zekrom, Reshiram, Gigalith, Seismitoad, Scolipede, Lilligant, Darmanitan, Carracosta, Zoroark, Cofagrigus, Reuniclus, Escavalier, Chandelure, Eelektross, Bisharp, the kino Volcarona and all related evolutions are all peak designs ( some of the best in the series), but everything outside of them is either completely forgettable, silly, downright bad, or some combination thereof. Not to mention very lackluster starters with poor final evolutions, and not a lot of interesting legendaries.