The cross section for coherent elastic neutrino-nucleus scattering (CE$ u$NS) depends on the response of the target nucleus to the external current, in the Standard Model (SM) mediated by the exchange of a $Z$ boson. This is typically subsumed into an object called the weak form factor of the nucleus. Here, we provide results for this form factor calculated using the large-scale nuclear shell model for a wide range of nuclei of relevance for current CE$ u$NS experiments, including cesium, iodine, argon, fluorine, sodium, germanium, and xenon. In addition, we provide the responses needed to capture the axial-vector part of the cross section, which does not scale coherently with the number of neutrons, but may become relevant for the SM prediction of CE$ u$NS on target nuclei with nonzero spin. We then generalize the formalism allowing for contributions beyond the SM. In particular, we stress that in this case, even for vector and axial-vector operators, the standard weak form factor does not apply anymore, but needs to be replaced by the appropriate combination of the underlying nuclear structure factors. We provide the corresponding expressions for vector, axial-vector, but also (pseudo-)scalar, tensor, and dipole effective operators, including two-body-current effects as predicted from chiral effective field theory. Finally, we update the spin-dependent structure factors for dark matter scattering off nuclei according to our improved treatment of the axial-vector responses.