We present an upgraded version of the SPY model, called SPY2 for version 2 of the scission point yield, to estimate mainly the yields and the kinetic energy distributions of fission fragments: The theoretical framework is similar to our previous version, i.e., a statistical scission point model, but this version is based on fully microscopic nuclear ingredients describing the fragments properties at the scission point. These include the static properties of some 7000 nuclei at 120 axial quadrupole deformations, such as binding energies, proton densities, single-particle level schemes, and states densities, coherently calculated within the constrained Hartree-Fock-Bogoliubov model on the basis of the Skyrme BSk27 interaction. The use of microscopic ingredients has been extended to the proton density distribution and the nuclear states densities. Considering realistic proton densities of fragments allows us to improve the definition of the scission point as well as the prediction of the kinetic energy distribution and to link the kinetic energy to the diffuseness of the fragments' proton density. New microscopic nuclear states densities improve the general coherence of the model, in particular regarding the inclusion of the odd-even pairing effect. In this updated SPY2 version, the calculation of the fission yields and kinetic energy distributions is significantly improved and found to be in relatively good agreement with experiments, at least qualitatively. A detailed study is performed for three well known fissioning systems, namely, thermal neutron induced fission of $^{235}\mathrm{U}$ and $^{239}\mathrm{Pu}$ and spontaneous fission of $^{252}\mathrm{Cf}$. A systematic analysis of the fission mode as well as mean fragments deformation and total kinetic energies has been performed for some 2000 fissioning nuclei with $78\ensuremath{\le}Z\ensuremath{\le}110$ lying between the proton and neutron drip lines.