We actually know some of these, or can make a strong guess.
As for Cubone, Marowak, and Kangaskhan: Yes, they were related. We know from the 2020 beta leaks that Cubone was originally part of a three-stage line, although only the back sprite has been uncovered (https://pbs.twimg.com/media/ESrtUrBVAAQZ39X.png). However this third evolution plainly mimics Kangaskhan and also closes the loop on Cubone’s lore. Cubone wears its mother’s skull and cries out for its mother, which we now know represents its separation from the third evolutionary line. Kangaskhan, for whatever reason, was redesigned as a stand alone entity. But its position on Giovanni’s team (the only non-Ground type he uses) implies some abandoned typing.
There is still some conjecture here but it all falls in to place perfectly and the back sprite clinched it enough for me.
As for Mew, the idea for Mew itself was not a last minute thing, only physically including it on the cartridge was. The lore for Mew is still quite present in the game: Scientists discovered Mew in South America (later revised to “the jungle”) where it was captured and brought back to the lab on Cinnabar Island. They came up with the name Mew on the spot. It was experimented on and specifically “gave birth” to Mewtwo, so we know Mew remained captive and alive at the laboratory. Mewtwo, as it developed, was too powerful and destroyed the laboratory, leaving only the burned mansion. Mewtwo fled to Cerulean Cave and the whereabouts of Mew are unknown.
This is the official story of R/B and what exactly Mew was or what it looked like was probably originally envisioned as a mystery to be resolved in the future. So even if Mew had not been included, Mewtwo still would have worked fine because we still knew the entity of Mew existed.
The last minute decision to add Mew to the game had to have come with some expectation for how to distribute it. Since there is no formal way to obtain it, they had to have at least acknowledged it would need to be activated externally at some point. Since the same idea was later used for Celebi (who NEVER saw an international release) they probably had the “event” idea on the table even in those early days.
For why Charizard and Gyarados weren’t made in to Dragon type, the answer for this is probably as straightforward as game balance. Game Freak did not know what to do with Dragon type. They knew they wanted a “super” type that resisted all the major elements to serve as an endgame challenge, but since Dragon was conceived as a defensive type for the player to overcome its offensive potential was just a non-factor. There’s only one Dragon type move with low, fixed base power. There are no new Dragon type Pokémon in Generation 2. Back then Pokémon was still designed along the conventions of traditional RPGs so the natural composition of the PokéDex was secondary to the construction of specific challenges for the player. Dragon was a “boss type” — if the player had access to Dragons early this would have had a limited effect.
I still hold on to the Venonat/Butterfree thing, personally. The visual similarities are too strong and we know lots of evolutions were mixed and matched and altered. I hope we can have that confirmed some day.
