There is a difference between quality and quantity.

I agree. We are thinking like a developed nation, but without the resources to carry this out. The difference between Starehe, Alliance and your village secondary school in terms of resources and organization is very huge. Even if KCPE is a flawed system, you cannot replace it with total chaos. Everyone would want to join Starehe, how would the Principal pick? KCPE should remain, and the govt should quickly build many basic schools so that those who don't score highly to go to 'made' schools are absorbed by the new schools.
For instance, in France, every student who finishes our equivalent of secondary school is entitled to a University education, and they have many universities all over the French provinces to educate all kids ...but to study at the prestigious grand ecoles, you have to pass some very hard exams. Eliminating KCPE won't solve anything, what needs to happen is to greatly increase secondary school capacity so that even if a student scores 50 out 500, they can attend a school somewhere.