The synthesis of Ti$_3$C$_2$T$_x$ (and Ti$_2$CT$_x$ alike) MXenes is performed with a new etching environment (FeF$_3$/HCl). Significant differences in terms of surface functionalization (including the insertion of iron cations between the MXene sheets), morphology, nature of impurities, water intercalation and reactivity are obtained in comparison with samples prepared by conventional HF or LiF/HCl etching methods. In particular, the new synthesis method allows modifying the reactivity of Ti$_3$C$_2$vs. water with improved selectivity towards the formation of TiO$_2$ anatase nanoparticles on the MXene sheets whereas rutile TiO$_2$ nanoparticles are favoured by the LiF/HCl method. The role of the Fe$^{n+}$ and Al$^{3+}$ cations inherent to this synthesis process in the inhibition of the anatase to rutile transformation is shown to be a key parameter. In addition, the MXene oxidation rate in water is also increased when the material is prepared with FeF$_3$/HCl compared to the LiF/HCl method owing to the surface modification of the MXene during the etching step. This oxidation rate can easily be tuned by adjusting the duration of immersion. This work expands the number of etching methods to form MXenes while offering new opportunities in the rationalized design of MXene@TiO$_2$ nanocomposite structures for future applications.