You assume we have the intelligence to anticipate everything.
The Greek word for this is hubris, "overweaning pride". In their tragedies, the protagonist's downfall is marked by his hubris in the face of the unknowable.
Breeds will only flourish as long as the conditions exist for which they were created.
A diverse gene pool contains the variety necessary to survive a broad range of conditions and the curveballs that environmental changes throw at it.
A little tinkering around the edges, to deter specific diseases, is not the same as designing organisms. Be careful what you wish for.