When we have a category $\mathcal C$, it is usual to define the category $\textrm{Ar}(\mathcal C)$ of morphisms of $\mathcal C$ as the one whose objects are the morphisms of $\mathcal C$ and whose morphisms are commutative squares: If $f:A\to B$ and $g:C\to D$ are elements of $\textrm{Ar}(\mathcal C)$, then a morphism from $f$ to $g$ is a pair of morphisms $(h:A\to C, h':B\to D)$ such that $h'f = gh$.
Therefore, since small categories and functors form a category, it would be expected that the morphisms between functors would be defined this way. But this is not the case, and instead what are used as the morphisms of functors are natural transformations. This is very strange and inelegant: why are morphisms between functors in usual categories defined one way but the ones in the category of categories defined differently?
Note that i'm not asking whether we can define morphisms the way i said, i know we can. I'm also aware of similar questions on this site but none answers where the different treatment of different categories comes from. (And to be honest i don't find any of the anwers in the other related questions satisfying either.)
Try defining morphisms between functors your way. You would end up with two additional functors and four categories. That might define a valid arrow category but it would be too general for our purposes.
– John Douma Mar 26 '23 at 15:47"It should be observed first that the whole concept of a category is essentially an auxiliary one; our basic concepts are essentially those of a functor and of a natural transformation (the latter is defined in the next chapter). The idea of a category is required only by the precept that every function should have a definite class as domain and a definite class as range, for the categories are provided as the domains and ranges of functors. "
– John Douma Mar 26 '23 at 16:08