For completeness, I did manage to create an inductive argument for this identity, though it is nowhere near the simplicity and elegance of the others here. I have also found a much simpler argument using finite differences; I'll leave the induction argument intact below the argument by polynomial theory:
Let $p(x)$ be a given integer-valued polynomial of degree $d$. The $n$th forward finite difference is given by
$$\Delta_p^n(x)=\sum_{i=0}^n(-1)^i{n\choose i}p(x+i)$$
If $n=d$ we get a constant, namely, the leading coefficient of $p(x)$ as taken in binomial form, i.e., $p(x)=\sum_ia_i{x\choose i}$. The formula stated in the question is an immediate consequence of these facts, taking $p(x)=\binom xn$.
Here is the proof by induction for anyone who might be interested:
For proof of $(1)$, use strong induction and start with $\binom {n+1}1 = 1 + \sum_{i=0}^{1-1}(-1)^i{k\choose i+1}{n-i\choose k} = 1+\binom n1 = n+1$. Assuming for $k = q$, we get
$${n+1\choose q} = 1+\sum_{i=0}^{q-1}(-1)^i{q\choose i+1}{n-i\choose q}$$
Establishing a base-case for $k=q+1$ is a matter of considering
$${q+2\choose q+1}=q+2 = 1+\sum_{i=0}^q(-1)^i{q+1\choose i+1}{q+1-i\choose q+1}=1+q+1 = q+2$$
after which we again make an assumption that our formula holds, this time for $n=r, r\ge q+1$: ${r+1\choose q+1}=1+\sum_{i=0}^q(-1)^i{q+1\choose i+1}{r-i\choose q+1}$. All that remains is to test the formula for $n=r+1$:
$$\begin{align}{r+2\choose q+1} &= 1+\sum_{i=0}^q(-1)^i{q+1\choose i+1}{r+1-i\choose q+1}\\
&= {r+1\choose q+1}+{r+1\choose q}\end{align}$$
By strong induction, we can use the formulas for $r+1\choose q+1$ and $r+1\choose q$ and write
$$\begin{align}{r+1\choose q+1}+{r+1\choose q}&=2+\sum_{i=0}^q(-1)^i{q+1\choose i+1}{r-i\choose q+1}+\sum_{i=0}^{q-1}(-1)^i{q\choose i+1}{r-i\choose q}\\
&=2+(-1)^q{r-q\choose q+1}+\sum_{i=0}^{q-1}(-1)^i\left({q+1\choose i+1}{r-i\choose q+1}+{q\choose i+1}{r-i\choose q}\right)\end{align}$$
This is a bit messy, but it works out well:
$$\begin{align}{q+1\choose i+1}{r-i\choose q+1}+{q\choose i+1}{r-i\choose q}&={q+1\choose i+1}{r-i\choose q+1}+\left[{q+1\choose i+1}-{q\choose i}\right]{r-i\choose q}\\
&={q+1\choose i+1}\left[{r-i\choose q+1}+{r-i\choose q}\right]-{q\choose i}{r-i\choose q}\\
&={q+1\choose i+1}{r-i+1\choose q+1}-{q\choose i}{r-i\choose q}\end{align}$$
Going in reverse, we now have
$$\begin{align}{r+1\choose q+1}+{r+1\choose q}&=2+(-1)^q{r-q\choose q+1}+\sum_{i=0}^{q-1}(-1)^i\left({q+1\choose i+1}{r+1-i\choose q+1}-{q\choose i}{r-i\choose q}\right)\\
&=2+(-1)^q{r-q+1\choose q+1}-(-1)^q{r-q\choose q}+\sum_{i=0}^{q-1}(-1)^i{q+1\choose i+1}{r+1-i\choose q+1}-\sum_{i=0}^{q-1}(-1)^i{q\choose i}{r-i\choose q}\\
&=2+\sum_{i=0}^{q}(-1)^i{q+1\choose i+1}{r+1-i\choose q+1}-\sum_{i=0}^{q}(-1)^i{q\choose i}{r-i\choose q}\\
&=1+\sum_{i=0}^{q}(-1)^i{q+1\choose i+1}{r+1-i\choose q+1}-{r\choose q}+1-\sum_{i=1}^{q}(-1)^i{q\choose i}{r-i\choose q}\\
&=1+\sum_{i=0}^{q}(-1)^i{q+1\choose i+1}{r+1-i\choose q+1}-{r\choose q}+1+\sum_{j=0}^{q-1}(-1)^j{q\choose j+1}{r-j-1\choose q}\\
{r+2\choose q+1}&=1+\sum_{i=0}^{q}(-1)^i{q+1\choose i+1}{r+1-i\choose q+1}\end{align}$$
Note that the last step follows from strong induction due to the original formula (with $r\ge q+1$)
$$\binom rq = 1+\sum_{i=0}^{q-1}{q\choose i+1}{r-1-i\choose q}$$