In his book, "Algebraic Topology - Homotopy and Homology", Switzer define (Definition 8.9) spectra functions as
$f:E\to F $ is a function if is a collection of cellular maps, $\{f_n:n\in\mathbb{Z}\}$ such that $f_{n+1}|_{SE_n}=Sf_{n}$.
In the definition he mentions that we can define compostion of spectra functions in the obvious way. But, right before the definition he says that this notion of function is not adequate to our purpose. Why is that the case? In which way this definition fails to be useful?
If you read the rest of the chapter, you will see that cofinal subspectra play a vital role in the theory of spectra. The goal is to define "maps" between spectra making cofinal subspectra isomorphic to the original spectrum. Functions of spectra are inadequate for this purpose, the inclusion function of a cofinal subspectrum into the original spectrum is no isomorphism. This is the reason why Switzer defines maps of spectra in Definition 8.12.