I mean, no one makes games about early colonial India or the Caribbean slave trade, it's not quite as much fun.
well, there is the (excellent) game puerto rico. it is definitely themed in that caribbean era, and the game makes heavy use of brown "colonists" who work your buildings and plantations.
It's possible that making the colonists brown could have been a coincidence. Sometimes, brown is just a nice neutral color.
Still, they could have gone with white or black, which are also neutral and fairly generic.
And if the coloring was on purpose because the designers aren't going to flinch from an unsavory history, then kudos for sticking to their guns. Other people (possibly even myself included) would have chosen a different color just to avoid offending someone. I don't know the truth behind the colonists' coloring, but I would not be surprised either way.
Oh, and Endeavor also has slavery. It doesn't detail the slave trade (thankfully), but you have the option of succeeding in the game by engaging in slavery. In fact, in one game, I and another player invested in slavery and then made sure that European control was split between us so that nobody could get enough influence to abolish slavery, since that would have weakened our empires. It was actually a pretty horrid reminder of how easily the colonials could engage in such a grotesque method.
As for gender in Dominion, I did note this weekend that the Duchess is also a mother. I don't recall any definite father figures in the card art. I mean, what is the Duke doing? Ruling a Duchy or something?