**Disclaimer:** this is not an answer to the question as I have no explanation for why people don't introduce natural transformations in the way explained in the question, but I am posting this in order to expand a comment I made. The comment was 
> this is the starting observation
> to make for introducing simplicial
> categories as a model for
> $\infty$--categories

Moreover, I am not a specialist neither of category theory nor of homotopy theory (and *a posteriori* of higher categories). 

The $2$-category of categories
------------------------------

The starting point is that the category $Cat$ of categories is actually a $2$-category. 
For any to objects (i.e. categories) $\mathcal C$ and $\mathcal D$ we have that 
$Hom_{Cat}(\mathcal C,\mathcal D)$ is itself a category. 

This is very transparent using the definition 
$$
Hom_{Cat}(\mathcal C,\mathcal D):=Hom_{t_{\geq1}(Cat)}(\mathcal C\times\Delta^1,\mathcal D)\,,
$$
where $\Delta^1=\Box^1=G^1$ is the arrow category $0\to 1$ and $t_{\geq 1}(Cat)$ is the underlying $1$-category of $Cat$. 

**Remark:** In general one can see a $2$-category $\mathcal C$ as a simplicial category replacing 
the $Hom$-categories by their nerves. 

In the case of $Cat$, we see that the $Hom$-category naturally appear as $1$-truncations of simplicial sets (one can replace here "simplicial" by "cubical" of "globular").  

The $3$-category of $2$-categories
----------------------------------

Le us now go to natural transformations of (strict) $2$-functors between (strict) $2$-categories. 
Given two such $2$-functors $F,G:\mathcal C\to\mathcal D$ one can see that a natural transformation 
$F\Rightarrow G$ is the same as a $2$-functors 
$$
\phi:\mathcal C\times G^2\to\mathcal D
$$ 
such that $\phi(-,0)=F$ and $\phi(-,0)=G$, where $G^2$ is the $2$-category with two objects $0$ and $1$ and such that 
$Hom_{G^2}(0,1)$ is the arrow category $G^1=(0\to 1)$. 

Therefore the "set" of $2$-functors is a naturally a $2$-category. 

**Remark:** as before we can then see any $3$-category as a simplicial/cubical/globular category by replacing 
the $Hom$-$2$-categories by their (simplicial/cubical/globular) nerves. 

In the case of $2-Cat$, we see that the $Hom$-$2$-category naturally appear as $2$-truncations of globular 
sets. 

Simplices, Cubes, and globes
----------------------------

The globe category $G$, the cubical category $\Box$ and the simplicial category $\Delta$ are known to be suitable [geometric shape to model higher structures][1]. Simplicial sets are good models for (weak) $\infty$-groupoids. It was proved ([by Jardine][2] ... with some improvement by Cisinski if I remember well) that cubical sets also provide a model for (weak) $\infty$-groupoids. 

I don't know any reference but I guess that the same holds for globular sets (which are quite more used by people working with automata). 

The $(n+1)$-category of $n$-categories
--------------------------------------

Let me consider the category $n-Cat$ of (strict) $n$-categories. A (strict) $n$-functor can be written as a functor 
$$
\phi:\mathcal C\times G^n\to\mathcal D
$$ 
such that $\phi(-,0)=F$ and $\phi(-,0)=G$, where $G^n$ is the $n$-category with two objects $0$ and $1$ and such that $Hom_{G^n}(0,1)$ is the $(n-1)$-category G^{n-1}$. 

Therefore the "set" of $n$-functors is a naturally a (strict) $n$-category, and thus $n-Cat$ is a (strict) $n+1$-category. It also naturally appears as a $n$-truncation of a globular category. 

The advantage of working with simplicial/cubical/globular categories
--------------------------------------------------------------------

Working directly with simplicial/cubical/globular categories has the following advantages: 

 1. it does allow to work directly with higher categories without going through an inductive process. 
 2. it allows to deal with **weak** $(\infty,1)$-categories, as simplicial/cubical/globular are models for weak $\infty$-groupoids (here $(\infty,1)$ stands for "$\infty$-categories such that $n$-arrows for $n\geq2$ are weakly invertible"). 


  [1]: http://ncatlab.org/nlab/show/geometric+shape+for+higher+structures
  [2]: http://hopf.math.purdue.edu/Jardine/cubical2.pdf