It's annoying. Especially when I play my legacy game, since I can't stop those ugly townies from infiltrating my family tree.
I allow my legacy Sims to beget as many children as they want, and I choose the next successor based on their progeny's traits (both physical and personality). I only play the active legacy though, so all un-chosen siblings get sent into 'Other Households' to make their own stories.
Now, while I may not actively play my reject descendants, I still like to check up on my tree every now and again to see how it's filling out. And, of course, my legacy's DNA is mixed with the ugliest townies around, with hardly a mention of any of the hot Sims I spent hours making.
My poor gene pool. No regard for pedigree whatsoever ...