The Mars Express Radio Science (MaRS) experiment on board Mars Express has been providing radio-occultation data since early 2004. The analysis method currently used to retrieve neutral atmosphere and ionosphere profiles is based on the resolution of a complex inverse problem. The solution to such a problem is obtained under strong assumptions on the atmosphere and the ionosphere and with some limitations. Here we developed a novel method for radio-occultation data analysis based on a direct approach which overcomes some of the difficulties related to the standard inversion. This new method is based on a numerical model of the atmosphere and the ionosphere of Mars computing the propagation of the radio waves from the spacecraft to the receiver on Earth. The main interest of such an approach lies in the intrinsic and coherent coupling between the neutral part and the ionized part of the planetary environment, which gives physical constrains on the retrieved profiles. We have applied this new method to radio occultation experiments performed by MaRS, and we present the results obtained in two different occultation configurations. We discuss the differences which emerge from the standard analysis and the gain that such a method can give to the analysis of planetary environments.