Having noted that $MM^T$ and $M^TM$ have the same eigenvalues, you seek the eigenvalues of the expectation values of each matrix. These can be very different, take for example $M$ of dimension $n\times 1$, and let each element of $M_{i}$ fluctuate independently between $M_i=+1$ and $M_i=-1$. Then $E[M^TM]$ has a single eigenvalue equal to $n$ while $E[MM^T]$ has $n$ eigenvalues equal to 1.
The sum of the eigenvalues of $E[M^TM]$ and $E[MM^T]$ is the same, which follows from the fact that, on the one hand, the trace of $MM^T$ equals the trace of $M^TM$, and on the other hand taking the trace commutes with taking the expectation value.