This is actually a question of linear algebra. The apparently inappropriate choice of sign stems from the fact that if $W$ is a (complex) vector space, and $A$ an endomorphism of $W$, then
$$ \ker (A-\lambda 1)\subset W $$
is the eigenspace for eigenvalue $(+\lambda)$.
In our case, we start with a real vector space, $V$, and an endomorphism $I$, satisfying $I^2=-1$. We extend it $\mathbb{C}$-linearly to an endomorphism $I_{\mathbb{C}}$ of $V\otimes \mathbb{C}$, and decompose the latter into $\pm i$ eigenspaces, usually called $V^{1,0}$ and $V^{0,1}$. The identity transformation decomposes into a sum of (eigenspace) projectors:
$$ 1 = \frac{1}{2}\left( 1 - i I_{\mathbb{C}}\right) +
\frac{1}{2}\left( 1 + i I_{\mathbb{C}}\right),$$
and we have a $\mathbb{C}$-linear isomorphism $V\subset V\otimes\mathbb{C}\to V^{1,0} = \ker\frac{1}{2}\left( 1 + i I_{\mathbb{C}}\right) $. Under this isomorphism $V\ni v\mapsto \frac{1}{2}(v-iIv)\in V^{1,0}$.
The complex structure $I$ induces a complex structure on the dual space $V^\vee$: this is the dual (transpose) endomorphism: $I^\vee \alpha(v)=\alpha(Iv)$. Its complexification, $I^\vee_\mathbb{C}$,
induces
an eigenspace decomposition of $V^\vee\otimes\mathbb{C}$.
For $\mathbb{R}^2 = (\mathbb{R}^2) ^\vee$
the "standard" complex structure $I$ is represented by the matrix
$\left(\begin{array}{rr}
0&-1\\
1&0\\
\end{array}\right)$, and $I^\vee$ by
$\left(\begin{array}{rr}
0&1\\
-1&0\\
\end{array}\right)$. Notice that $I$ is skew-symmetric and the $\pm i$ eigenspaces of $I$
and $I^\vee$ are interchanged!
If you apply the above isomorphism $V\simeq V^{1,0}$ ( resp. $V\simeq V^{0,1}$)
to the first standard basis vector $e_1\in\mathbb{R}^2$, you will get
$$\left\{
\frac{1}{2}
\left(
\begin{array}{r}
1\\
-i\\
\end{array}
\right),
\frac{1}{2}
\left(\begin{array}{r}
1\\
i\\
\end{array}\right)
\right\},
$$
an eigenbasis (for $I_\mathbb{C}$) of $\mathbb{C}^2$, where the eigenvalues are ordered
$\{+i,-i\}$.
Its dual basis is
$$
\left\{
\left(\begin{array}{r}
1\\
i\\
\end{array}
\right),
\left(\begin{array}{r}
1\\
-i\\
\end{array}
\right)
\right\},
$$
consisting of eigenvectors for $I^\vee_\mathbb{C}$, with eigenvalues $\{+i,-i\}$.
Now rephrase all of the above in terms derivations. The $\mathbb{C}$-isomorphism $V\simeq V^{1,0}$ gives you $\frac{\partial}{\partial x}\mapsto \frac{1}{2}
\left(\frac{\partial}{\partial x} - i \frac{\partial}{\partial y}\right)$, and
$$\left\{ \frac{1}{2}\left(\frac{\partial}{\partial x} - i \frac{\partial}{\partial y}\right),
\frac{1}{2}\left(\frac{\partial}{\partial x} + i \frac{\partial}{\partial y}\right)
\right\}$$
is a $\mathbb{C}$-basis of $\mathbb{R}^2\otimes \mathbb{C}$, dual to
$\left\{dx + i dy, dx-idy \right\}$. As the latter is conventionally denoted by
$\left\{dz,d\overline{z}\right\}$, it is natural to denote its dual basis by $\left\{ \frac{\partial}{\partial z}, \frac{\partial}{\partial \overline{z}}\right\}$.
Notice that with this convention
$dz\left(\frac{\partial}{\partial \overline{z}} \right) =0$ and
$d\overline{z}\left(\frac{\partial}{\partial \overline{z}} \right) =1$, which is highly desirable, as mentioned in the comments.
ADDENDUM
In sum, we have to make a compatible choice of:
1) Eigenvectors of $I$
2) Eigenvectors of $I^\vee$.
We tend to put bars on the eigenvectors with eigenvalue $(-i)$. Eigenvectors are determined up to a nonzero scalar, so a priori we have to choose 4 of these (in $\mathbb{C}^2=\mathbb{R}^2\otimes\mathbb{C}$ ).
However, the conditions:
a) $\frac{\partial}{\partial \overline{z}} =
\overline{\frac{\partial}{\partial z}}$
b)$\left\{ \frac{\partial}{\partial z}, \frac{\partial}{\partial \overline{z}}\right\}$
is a dual $\mathbb{C}$-basis to $\left\{dz,d\overline{z}\right\}$
leave us only with the freedom of replacing $\frac{\partial}{\partial z}$ by a scalar multiple.
As an example, if you take the complex structure
$\left(\begin{array}{rr}
-1&-2\\
1&1\\
\end{array}\right)$, then, up to that single scalar ambiguity, we have
$$ dz = dx+ (1+i)dy, \ d\overline{z} = dx + (1-i) dy$$
$$\frac{\partial}{\partial z}=\frac{1}{2}\left( (1+i)\frac{\partial}{\partial x} -
i \frac{\partial}{\partial y}\right),
\frac{\partial}{\partial \overline{z}}=\frac{1}{2}\left( (1-i)\frac{\partial}{\partial x} +
i \frac{\partial}{\partial y}\right)$$