In the book by Chuang and Nielsen they prove that controlled U operations can be made out of CNOTs and single qubit gates. But then they go on to prove that they are universal by showing that every n by n matrix can be decomposed into two level matrices and then to CNOTs and single qubit gates.  But if so, then why can't we prove this way that controlled U can be too, decomposed to them. Since a controlled U is after all an n by n matrix. Why is there a separate proof for them?