A lot of people like to praise generation 1 for having great Pokémon designs, and while I really like some of the designs (such as Lapras, Bulbasaur and Eevee), I think it was overall the worst generation in that regard. Not only design-wise, but they also made some decisions (due to hardware issues or simply lack of identity) that don't fit anymore with what the series has become. Here are some examples:
- Ekans is just a snake. No more, no less. Its name is also just "snake" backwards.
- Nidoran Male and Female are two different species. I guess the Game Boy couldn't handle sprite differences based on gender.
- Nidorina and Nidoqueen can't breed. Both Nidoran, Nidorino, and Nidoking can. That's still true in newer games, despite it making absolutely no sense at all.
- Dugtrio is the laziest Pokémon ever created. It literally is three Digletts together, not a single new feature added to it. I can understand Magneton being three Magnemites together because that's what magnets do, but moles don't do that as far as I'm concerned.
- Psyduck and Golduck are pure Water-types, despite Psyduck literally being an amalgamation of "Psychic" and "Duck".
- A lot of Pokémon are literally wearing clothes. It's not like they have clothes-like aspects, they're clearly using human clothes. Jynx, Hitmonchan, Mr. Mime, Machoke and Machamp all wear human clothes.
- Kadabra and Alakazam are holding spoons all the time. Kanto must have a pretty big spoon factory. It's not like the spoons are part of the Pokémon either, they're clearly just holding them.
- Graveler evolving into Golem makes no sense. Graveler is a living rock. Golem is a reptile "stuck" inside a rock.
- Seel is just a seal. They just changed a letter.
- Dewgong is just a Dugong. They just changed two letters.
- Muk is just a larger Grimer. And they're both just boring piles of mud.
- Krabby is just a Crab. Its name in Japanese is literally "Crab". The only inspiration for its design is a crab.
- Electrode is a terrible evolution. It would have been much more interesting to go from Voltorb (a Poké Ball), to a Great Ball and then to an Ultra Ball. Instead, they just flipped it around and gave it a mouth.
- Mr. Mime and Jynx look too much like humans. It's weird to even call them Pokémon.
- Venomoth is just a regular moth. So creative.
- Exeggcute is a bunch of eggs. Just eggs with faces.
- Kangaskhan is born with a baby in its pouch. I guess they didn't think that through.
- Goldeen is just a goldfish. There's absolutely nothing interesting about it.
- Dragonair and Dragonite don't even look remotely similar. Why are they part of the same evolutionary family?
Maybe st Pokemon are just twists on animals, and Gen 1 is obviously going to be the most basic part of this concept. Personally, the animal ones are the best. It gets stupid with Mr Mime, Jynx and Voltorb/Electrode, but there's Pokemon like this in every Gen.
Other than that some of your logic is a bit off.
Nidorina/Nidoqueen has confused me as well, but I think it's how the breeding system works in game. If they did, I don't think they'd ever produce male Nidoran, which would make less sense. Had they been introduced Gen 4 or later, Nidoran would have been a single Pokemon.
Kadabra and Alakazam seem to get the spoons when they evolve, so looks like they are a part of them.
For your evolution differences, Metapod looks nothing like Butterfree but it still works. Plus Dragonite does resemble Dragonair, but has a colour change and arms and legs. Still the same serpent shape though.