We report the first longitudinal/transverse separation of the deeply virtual exclusive $pi^0$ electroproduction cross section off the neutron and coherent deuteron. The corresponding four structure functions $dsigma_L/dt$, $dsigma_T/dt$, $dsigma_{LT}/dt$ and $dsigma_{TT}/dt$ are extracted as a function of the momentum transfer to the recoil system at $Q^2$=1.75 GeV$^2$ and $x_B$=0.36. The $ed to edpi^0$ cross sections are found compatible with the small values expected from theoretical models. The $en to enpi^0$ cross sections show a dominance from the response to transversely polarized photons, and are in good agreement with calculations based on the transversity GPDs of the nucleon. By combining these results with previous measurements of $pi^0$ electroproduction off the proton, we present a flavor decomposition of the $u$ and $d$ quark contributions to the cross section.