An important challenge in the field of topological materials is to carefully disentangle the electronic transport contribution of the topological surface states from that of the bulk. For Bi$_2$Te$_3$ topological insulator samples, bulk single crystals and thin films exposed to air during fabrication processes are known to be bulk conducting, with the chemical potential in the bulk conduction band. For Bi$_2$Te$_3$ thin films grown by molecular beam epitaxy, we combine structural characterization (transmission electron microscopy), chemical surface analysis as function of time (x-ray photoelectron spectroscopy) and magnetotransport analysis to understand the low defect density and record high bulk electron mobility once charge is doped into the bulk by surface degradation. Carrier densities and electronic mobilities extracted from the Hall effect and the quantum oscillations are consistent and reveal a large bulk carrier mobility. Because of the cylindrical shape of the bulk Fermi surface, the angle dependence of the bulk magnetoresistance oscillations is two-dimensional in nature.