We calculate a low-frequency surface impedance of a dirty, s-wave superconductor with an imperfect surface incorporating either a thin layer with a reduced pairing constant or a thin, proximity-coupled normal layer. Such structures model realistic surfaces of superconducting materials which can contain oxide layers, absorbed impurities or nonstoichiometric composition. We solved the Usadel equations self-consistently and obtained spatial distributions of the order parameter and the quasiparticle density of states which then were used to calculate a low-frequency surface resistance $R_s(T)$ and the magnetic penetration depth $λ(T)$ as functions of temperature in the limit of local London electrodynamics. It is shown that the imperfect surface in a single-band s-wave superconductor results in a non-exponential temperature dependence of $Z(T)$ at $T\ll T_c$ which can mimic the behavior of multiband or d-wave superconductors. The imperfect surface and the broadening of the gap peaks in the quasiparticle density of states $N(ε)$ in the bulk give rise to a weakly temperature-dependent residual surface resistance. We show that the surface resistance can be optimized and even reduced below its value for an ideal surface by engineering $N(ε)$ at the surface using pairbreaking mechanisms, particularly, by incorporating a small density of magnetic impurities or by tuning the thickness and conductivity of the normal layer and its contact resistance. The results of this work address the limit of $R_s$ in superconductors at $T\ll T_c$, and the ways of engineering the optimal density of states by surface nano-structuring and impurities to reduce losses in superconducting micro-resonators, thin film strip lines, and radio frequency cavities for particle accelerators.