:EDIT:
I was writing a comment that I don't think there's going to be a definitive answer on this question, that the question is akin to "Why do we draw free body diagrams for an engineering analysis?" or, "Why do we factor polynomials?"
I then realized that this question is very much like, "Why do we factor polynomials?" Factoring a polynomial is useful because it reduces a higher order expression into products of first order expressions.
Translating a system's dynamics equations into a series of coupled first order linear ODEs does the same thing. This still isn't an answer more than the original answer below, just a reinforcing concept that we generally choose to start with the simplest representation available because it affords the simplest means of solving the problem.
:Original post:
Dynamic systems are usually represented that way because it's a "canonical form" for control problems.
A canonical form is advantageous because, if you can express your problem in a canonical format, you get to use all of the preexisting tools that have been developed to analyze and solve that problem.
Consider standard interfaces in other settings - I can connect my watch, a printer, an Arduino, a game controller, etc. to my computer because they all use the USB standard interface. I don't need to keep a kit full of proprietary cables, or have a laptop that has a bank of proprietary connectors, thanks to the standard interface.
Similarly, I don't need a "toolkit" of methods to evaluate or solve controls problems if I can get to the canonical control form. In particular, some important "standard tools" include:
- Eigenvalues of $\bf{A}$ reveal system stability,
- Standard methods to check for observability and controllability,
- The separation principle, which shows that you can design the controller and observer independently,
- Standard method for modifying system response (pole placement),
- Scalability from single input, single output (SISO) systems to multi-input, multi-output (MIMO) systems, and the associated linear quadratic regulator,
- Relatively easy to construct a Kalman filter from that representation (if the Kalman filter has $\hat{x}_{k|k-1} = F_k \hat{x}_{k-1|k-1} + B_k u_k$, then you can use $F_k = (I + A\Delta t)$ and $B_k = B \Delta t$, and then $H_k = C$).
This is a list of things that rely on your system to be in the form:
$$
\dot{x} = Ax + Bu \\
y = Cx + Du \\
$$
If you want (or need) to express your problem differently then the tools I've mentioned above are no longer valid and you need to find/make equivalents for your application. The hard part there isn't just finding something that "looks like" the tools mentioned, or that has "similar looking step responses," but proving things like BIBO stability, etc. This is the hard work that has been done for you already if you (can) use the existing tools.