I think one of the interesting things about trying to do a game that encompasses all of human history is that you have to try and answer a question which historians, especially nowadays, generally don't even try to answer - specifically, what are the actual driving/motivating factors in human history? What's the underlying theory and model of what drives human civilisation?
A lot of games work on it purely in terms of separate factions/cultures which thrive or not on the basis of access to resources, because those are fairly simple to represent in game terms, possibly with some sort of "culture" metric or "wonders" that allow alternative ways of turning resources into achievement. Civilisation definitely works on that premise. I'm not sure if that's the ideal model for a whole-of-history game, though - it can make sense for a strategy game of a few years or a couple of centuries, but the idea that you have a single state that goes from the stone age to modernity is something that we have precisely nil examples of. I feel like having ways of evolving the state of the world much more through the game would be helpful; you might lose the "this is my team for now and always" feeling, but you might gain something in epic feel if you managed to build a modern world on the ruins of what had gone before. I'm wondering if something like smallworld's mechanics for switching out old factions and starting new ones might be interesting to explore for this?
I think the other area to think about is win conditions: I don't know if one actually should premise human history spanning games on the idea of "the winner is when one player becomes master of the earth". It's quite a colonial era aspiration that I'm not sure necessarily works in the long run - or at least, it might be the goal of some factions but not others. Having randomised or variable victory conditions might be fun for this sort of game - especially if your victory condition involved the other players too which could lead to good player interactions. So if one player got bonuses depending on e.g. the total state of scientific research at game end, another one wanted to make the highest average living standards, and the third one was out to conquer the world, that would lead to some interesting strategic trade-offs.