When a layer of fluid is oscillated up and down with a sufficiently large amplitude, patterns form on the surface, a phenomenon first observed by Faraday. A wide variety of such patterns have been observed from regular squares and hexagons to superlattice and quasipatterns and more exotic patterns such as oscillons. Previous work has investigated the mechanisms of pattern selection using the tools of symmetry and bifurcation theory. The hypotheses produced by these generic arguments have been tested against an equation derived by Zhang and Vinals in the weakly viscous and large depth limit. However, in contrast, many of the experiments use shallow viscous layers of fluid to counteract the presence of high frequency weakly damped modes that can make patterns hard to observe. Here we develop a weakly nonlinear analysis of the full Navier-Stokes equations for the two-frequency excitation Faraday experiment. The problem is formulated for general depth, although results are presented only for the infinite depth limit. We focus on a few particular cases where detailed experimental results exist and compare our analytical results with the experimental observations. Good agreement with the experimental results is found.