We investigate the relationship between molecular order and charge-transport parameters of the crystalline conjugated polymer poly(3-hexylthiophene) (P3HT), with a particular emphasis on its different polymorphic structures and regioregularity. To this end, atomistic molecular dynamics is employed to study an irreversible transition of the metastable (form I') to the stable (form I) P3HT polymorph, caused by side-chain melting at around 350 K. The predicted side-chain and backbone-backbone arrangements in unit cells of these polymorphs are compared to the existing structural models, based on X-ray, electron diffraction, and solid-state NMR measurements. Molecular ordering is further characterized by the paracrystalline, dynamic, and static nematic order parameters. The temperature-induced changes of these parameters are linked to the dynamics and distributions of electronic coupling elements and site energies. The simulated hole mobilities are in excellent agreement with experimental values obtained for P3HT nanofibers. We demonstrate that a small concentration of defects in side-chain attachment (90% regioregular P3HT) leads to a significant (factor of 10) decrease in charge-carrier mobility. This reduction is due to an increase of the intermolecular part of the energetic disorder and can be traced back to the amplified fluctuations in backbone-backbone distances, i.e., paracrystallinity. Furthermore, by comparing to poly(bithiophene-alt-thienothiophene) (PBTTT) with its higher hole mobility, we illustrate how transport in P3HT is disorder limited as a result of its side-chain structure.