CC With Good Genes

[Majick]

Just so you know, the Dr. Vu machine doesn't outdo the genetics your Sim will pass on when it has kids, it just makes them tolerable for THAT generation.  The genetics they're born with STILL carries over to the next generation.

It sucks.  Best thing I can suggest is just keep making sims in CAS with the first face, tweaking here and there if/when needed, until the genetics work themselves out.  It's what I do.