One key number-theoretical reason for starting the sequence $(0,1)$ instead of $(1,1)$ is that it makes the _divisibility_ property of the Fibonacci sequence more straightforward to state; i.e., that $F_k$ divides $F_{nk}$ for any $k,n$. If you start with $F_0=1$ instead of $F_0=0$ then this breaks down (for instance, in that numbering $F_2=2$ but $F_4=5$) and a lot of results have to be presented with indices shifted. This has to do, roughly with the representation of $F_n$ as $\frac{1}{\sqrt{5}}\left(\phi^n-\varphi^n\right)$ (with $\varphi=\frac{1}{\phi} = \phi-1$); the fact that the exponents 'match up' with the index leads to straightforward arguments for the various divisibility properties.