I also don't get the popularity of prehistoric phases, it is just beyond the scope and scale of such games. Even in Humankind it's just like ten turns of an obligatory filler because well, what can you do with a civ scaled map in terms of tiny nomadic tribal society? By definition you can't exploit or transform the map tiles in any way, or have cities, science, government, organised religion, anything really.
In the regard of a nomadic gameplay a la Humankind you have a point, but a Prehistoric Era is not by default that. Neither must lack the elements you pointed.
* Prehistory is not just Paleolithic or Mesolithic nomadic bands of people.
* Many of CIV's technologies and civics present as ancient are prehistoric.
* For CIV's gameplay model the relevant base is the sedentary aspect that allow us to pull back to Neolithic-Chalcolithic agrarian, pastorial and fishing based permanent settlements. Even the earliest cities (or proto-cities) of these period were already in thousands of inhabitans.
* CIV also have civs like Shoshone and Maori that mostly would fit into a level equivalent to Neolithic-Chalcolithic societies.
* Chiefdom and Tribal Federations are forms of goverment, again CIV already have tribal leaders.
* Half of CIV's eras "Science" would not be Science in its formal definition.
* There are civs in game that never developed "organized religion" but at the same time we have the pantheons and there is not reason to deprive them from beliefs, cults and shriners, even the earliest form of temples/monuments are thousand of years older than any "formal religion".
So, probably Humankind should have named their prologue era "Paleolithic-Mesolithic" and/or CIV should stop making us research techs/civs and infrastructure that predated historical urban societies. Still Neolithic-Chalcolithic societies have settlements, production infrastructure, trade, beliefs, technology advances, social organization and warfare everything CIV's gameplay model needs to work.