Each gen may have its stinkers, but I like how the dex tries to follow the same design philosophy as the region they're in or the theme the games are trying to push.

Gen 1 focuses a lot on science and eugenics, so a lot of the dex is part poison to represent toxic waste and some Pokemon are the result of genetic experiments/revitalization. Gen 2 is a lot more traditional and japanese-inspired, so a lot of the mons are more basic in design or pull heavily from japanese mythology. Gen 3 focuses a lot on the dangers of nature, so a lot of the designs are wilder, more savage-looking animals. Sinnoh is a slower, snowy, mountainous region, so there are a lot of bigger, bulkier Pokemon. Unova is a very industrialized region and is a direct reference to Gen 1, so it pulls most of its dex from the Gen 1 dex and modernizes it. Kalos is France, beauty, etc, so a lot of mons look fruity and flamboyant. Gen 7 is Hawaii, so a lot of the mons look very jolly, playful and exotic.

Without trying to place one gen above the other, I think this is what sets Pokemon apart from similar franchises. The attention to detail and the general coherence and consistency in the themes and design philosophy.