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What you're concerned about is called inbreeding depression which is "the reduced biological fitness in a given population as a result of inbreeding, or breeding of related individuals. Population biological fitness refers to an organism's ability to survive and perpetuate its genetic material. Inbreeding depression is often the result of a population bottleneck. In general, the higher the genetic variation or gene pool within a breeding population, the less likely it is to suffer from inbreeding depression."
From what I've read, for the game devs to make this realistic and avoid inbreeding depression the minimum viable population would have to be very large, probably larger than any civilization built in game so far. I may be incorrect but the number I keep seeing is 5,000. You would need 5,000 random organisms from a given species for them to be able to reproduce (without any intervention - people keeping track of family trees and who's mating with who). Do you want to start your game with 5,000 nuggets to keep track of? No, me either.
I do hear what you're saying. When you really sit there and think about it, it's a little odd/funny/gross. However, I think any game/movie/story etc. you enjoy will have these sorts of issues. They just aren't as glaring to you. I can tell you for certain, there aren't any simulations that perfectly (besides illustris maybe, but that doesn't simulate life) immitate real world physics, biology or any other kind of science. Probably the most important thing you take away from this is Suspension of Disbelief: "a willingness to suspend one's critical faculties and believe something surreal; sacrifice of realism and logic for the sake of enjoyment."
I don't think the devs are going to address this issue but maybe I'm wrong.
The incest isn't really what bother me because like you say it can happens what bother me is to have only one couple and my tribe will be only from this couple. Is there a perticular reason why the dev would restrict it to just 2 pawns to establish a civilisation?
Age of Empire didn't started with only 2 pawns neither and it was a great game that I hope this game will follow.
The reason why they started with 2 is because you are A GOD and the first 2 humans were Adam (Adahy) and Eve (Elu).
As most Christians know, Adam and Eve have 3 sons: Cain, Abel and Seth (all males), which means all Christians are offspring of Gay Incest coupling of Cain Abel and Seth before God patched the game and prevented homosexuals from having kids.