If that's what you take out of the various mammalian genome projects you surely miss out.
Still, I understand what you are trying to say.
How would you do it if you were the designer? What are the design flaws in your make believe genome you describe?
Create a system flexible enough to handle a constantly changing environment (i.e. evolution).
Constant tinkering with the creation is for second rate software engineers. And even those guys could splice chromosomes together with a bit more skill.