Quantum simulation offers a powerful approach to studying quantum field theories, particularly (2+1)D quantum electrodynamics (QED${}_3$) with Wilson fermions, which hosts a rich landscape of physical phenomena. A key challenge in lattice formulations is the proper realization of topological phases and the Chern-Simons terms, where fermion discretization plays a crucial role. In this work, we highlight the differences between staggered and Wilson fermions coupled to $\mathrm{\text{U}}(1)$ gauge fields in the Hamiltonian formulation. We analyze why staggered fermions fail to induce (2+1)D topological phases, while Wilson fermions admit a variety of topological phases including Chern insulator and quantum spin Hall phases. Additionally, we uncover a rich phase diagram for the two-flavor Wilson fermion model in the presence of a chemical potential. Our findings resolve existing ambiguities in Hamiltonian formulations and provide a theoretical foundation for future quantum simulations of lattice field theories with topological phases. We further outline connections to experimental platforms, offering guidance for implementations on near-term quantum computing architectures. A complementary presentation of the analytical calculations, the identification of robust topological structure and response, and extensive numerical results is contained in a joint submission.