To fix the idea, let's consider a spin glass Hamiltonian $H(\sigma,J)$, where $\sigma$ are the spins and $J$ is a random variable with distribution $p(J)$ representing the couplings.
An example is the Edwards-Anderson spin glass:
$$H = - \sum_{\langle i,j \rangle} J_{ij} \sigma_i \sigma_j$$
where $J_{ij}$ are Gaussian random variables.
The annealed free energy is
$$F_a = -\frac{1}{\beta} \ \log \int dJ \ p(J) \int d\sigma\ e^{-\beta H(\sigma,J)} = -\frac{1}{\beta} \log[\overline{Z(\beta,J)}]\tag{1}\label{1}$$
while the quenched free energy is
$$F_q = -\frac{1}{\beta} \int dJ\ p(J) \ \log \int d\sigma\ e^{-\beta H(\sigma,J)} =-\frac{1}{\beta} \overline{\log[Z(\beta,J)]}\tag{2}\label{2}$$
In \ref{1} you are treating $J$ and $\sigma$ on equal footing, so that $J$ becomes just another degree of freedom: $J$ and $\sigma$ fluctuate "together".
You could actually define an "effective Hamiltonian"
$$\tilde H_\beta(\sigma,J) = H-\frac 1 \beta \log p(J)$$
and write
$$F_a = -\frac{1}{\beta} \log \int dJ d\sigma e^{-\beta \tilde H_\beta(\sigma,J)}$$
In \ref{2}, the situation is different, because you are
- First, creating a realization of the system with a certain (fixed) disorder $J$, and calculating the corresponding free energy.
- Then, averaging over all the free energies obtained this way with respect to the disorder $J$.
The variables $J$ and $\sigma$ are not anymore on equal footing: $J$ is fixed when you average over $\sigma$, and this is the crucial point.
References