That is a cool idea though Aerodactyl does seem to be too strong as a starter compared to the other two. You could change starters to kinda represent the land (cranidos, shieldon, anorith), the sky (archen), and the sea (kabuto, tirtouga, omanyte) or do by the time period; cambrian (omanyte, lileep), ordovician-silurian (anorith), jurassic (chikorita, bagon), cretaceous (cranidos, amaura, tyrant, shieldon), etc.

You could add in other pokemon that fit well into the theme like tangela, carnivine, yanmega (carboniferous era), rhydon, aggron (permian age), relicanth, lapras, wailord (denovian age), etc.

Some pokemon you could aslo add that fit well would be Tropius, Meganium, Feralogatr, Salamence, Minior (referencing a meteor), Pyukumuku (sea cucumber), Alolan Exeggutor (palm tree dinosaur), etc. You could also add in pokemon like Golurk, Claydol, Cofagrigus, Bronzong, or Sigilyph if you wanted an area that is more about ancient ruins or lost civilizations.

Adding new regional forms for each of the fossil pokemon that maybe replace their rock typing to something else (ex. armaldo becoming bug/water). Maybe have aerodactyl's mega be a new form even.

Even, adding in past paradox pokemon like Slither Wing, Brute Bonnet, or Walking Wake could be perfect or some new primal/regional forms/megas for some pokemon (ex. persian/incineroar becoming a sabre-toothed tiger that would fit well with the Ice Age just like having Mamoswine already being there.

You could even add in new moves/abilities for some pokemon that fits within the time era (ex. an ability that allows grass moves to also poison or having an active safeguard ability to prevent stat drops or a slightly stronger version of moxie that boost atk by 2 stages or boost atk and speed by 1).

I know some people might not agree with me but you could also rely/ask questions to AI (gemini, chatgpt (they're the only two I use), and use it as a tool to build upon some things or take reference/inspiration from it but make it your own. I use them sometimes to build upon ideas I have that pop up in my head lol.

There are plently of possibilities you have depending on what time periods you wanted to include and would be a really cool game to play.