Equivalence of Categories and of Their Functor Categories
Recall that $\mathsf{Cat}$ (the category of all small categories) is a $\mathsf{Cat}$-enriched category. Thus we have internal hom functors. Let me spell this out explicitly:
You should be able to check that $A \mapsto [A,C]$ (this is what you write as $C^A$) is a contravariant $\mathsf{Cat}$-endofunctor of $\mathsf{Cat}$ , i.e. that we have functors $[B,A] \to [[A,C],[B,C]]$, $F \mapsto F^*$ which commute with the identity and composition. As such, it preserves equivalences by formal nonsense.
Similarly, $A \mapsto [C,A]$ provides a covariant $\mathsf{Cat}$-endofunctor of $\mathsf{Cat}$, i.e. have functors $[A,B] \to [[C,A],[C,B]]$, $F \mapsto F_*$ which commute with the identity and composition. Again it follows that equivalences are preserved.
Maybe I'm missing something, but I would say that $C^A$ and $C^B$ are indeed equivalent.
In fact, if we have an equivalence of categories between $A$ and $B$, that means we have a couple of functors
$$ F: A \longrightarrow B \qquad \text{and} \qquad G : B \longrightarrow A \ , $$
together with a couple of isomorphisms of functors
$$ \varepsilon : FG \longrightarrow \mathrm{id}_B \qquad \text{and} \qquad \eta : \mathrm{id}_A \longrightarrow GF \ . $$
So, I'm lost: why can't you build another equivalence of categories just like this?
$$ F^* : C^B \longrightarrow C^A \qquad \text{and} \qquad G^* : C^A \longrightarrow C^B \ , $$
where
$$ F^*(\phi) = \phi\circ F \qquad \text{and} \qquad G^* (\psi ) = \psi \circ G \quad \text{?} $$
EDIT 1. In the same vein: why
$$ F_*: A^C \longrightarrow B^C \qquad \text{and} \qquad G : B^C \longrightarrow A^C \ , $$
defined as
$$ F_*(\phi ) = F\circ \phi \qquad \text{and} \qquad G_*(\psi ) = G \circ \psi $$
do NOT define another equivalence of categories? As far as I can see, there is no "cube" that needs to commute anywhere. Am I wrong?
EDIT 2. More details for the first case. I should have defined $F^*$ and $G^*$ on morphisms too. Ok, let's do it like this: for any natural transformation of functors $f:\phi_1 \longrightarrow \phi_2$ (a morphism of $C^B$), define
$$ F^*(f)_a = f_{Fa} : \phi_1(Fa) \longrightarrow \phi_2(Fa) \ . $$
And analogously for $G^*$.
Then, the natural isomorphism $\eta$ induces another natural isomorphism
$$ \eta^* : \mathrm{id}_{C^A} \longrightarrow F^*G^* $$
as follows: for any functor $\psi : A \longrightarrow C$, you've got a natural transformation
$$ \eta^*(\psi ) : \psi \longrightarrow \psi \circ G\circ F $$
defined as
$$ \eta^*(\psi )_a = \psi (\eta_a) : \psi (a) \longrightarrow \psi (GFa) $$
This $\eta^*(\psi)$ is indeed a natural transformation of functors (that is, a morphism of $C^A$): for any $f: a \longrightarrow b$ you've got the needed commutative diagram just applying $\psi$ to the commutative diagram you obtain from the fact that $\eta$ is a natural transformation.
You have to check that also $\eta^*$ is a natural transformation and isomorphism. At this point some diagrams are needed. Let's see if I'm able to put here a link to the right pdf file.
EDIT 3. I forgot to tell you: here and there you'll probably need the word "small" for these categories of functors being actual categories. For instance, if I remember correctly (I don't have my Mac Lane with me right now), you'll need $C$ to be small for $A^C$ and $B^C$ to be categories. Otherwise, you invoke some bigger universe and it will do. (I guess.) :-)