Posting via a phone, so don't mind the typos, please...
What the Clans did during the Wars of Reaving bothers me too. They essentially bottlenecked their selves - again.
For a society obsessed with genetics, the clans make dumb decissions from a genetically-inclined point of view. Yes, it's only a game, but it's science fiction that prides itself on being a somewhat harder brand of science fiction whenever possible, so I feel free to complain. In this instance, the Home Clans have done a lot of hard work to eliminate genetic diversity whenever possible throughout the Wars of Reaving. Mass sterilization, orbital obliteration of population groups who hold different values and ideas, on top of their "gene puddle" of a warrior caste.
The warrior caste is effectively a population on a self-imposed island. After a few hundred years, we're already getting to see what happens to populations like that, through bloodhouses that have exhausted their selves (like often with the Mandrills), to individuals who exhibit insanity. Insanity is said in canon to be "rare among the Clans", yet an instance of it led to the wars of reaving, in the person of the Bloody IlKhan. The signs of the clans' "great experiment" coming to an end are there to be discerned. One doesn't even have to look hard for them, the major plot points are rife with them.
Makes one wonder what the Home Clans will bring to the game table next. Perhap they'll break through their own self imposed limits on the genetic engineering techniques they use. They may have to, considering the damage they have done to their selves through the centuries.