Incoherent scatter radar measurements rely on the application of a priori parameters from empirical models to initialize the analysis of incoherent scatter spectra. Currently, there is a need to transform ionosphere models to enable reliable space weather predictions through data assimilation of observations. Very often the data assimilation relies on electron densities measured with incoherent scatter radars. Erroneous a priori parameters would lead to the assimilation of flawed and physically inconsistent data depending on the ionospheric model. It might therefore be beneficial to assimilate the entire radar spectrum and infer the plasma parameters from the assimilated spectrum by applying the a priori parameters as given by the model. To assess the potential assimilation of incoherent scatter spectra into models, we investigate synthetic EISCAT incoherent scatter spectra calculated from TIE-GCM results. At F1 region altitudes, the atomic-to-molecular ion ratio strongly affects the shape of the incoherent scatter spectrum. Since the vertical profiles of the atomic-to-molecular ion ratio are distinctly different in the EISCAT a priori model and TIE-GCM, the assimilation of single plasma parameters induces additional, unbalanced forces into the model. A similar problem arises in the E region due to different ion-neutral collision frequency profiles. These problems could be solved by assimilation of the entire incoherent scatter spectrum followed by an in-model evaluation of the plasma parameters. We demonstrate the effect of different a priori profiles on the spectral analysis and how the derived plasma parameters are changing when leveraging a more comprehensive approach of using forward modeling with TIE-GCM.