Mesoscale aggregates arising from the separation of ionic and alkyl groups into polar and nonpolar regions have been observed for a variety of ionic liquids (ILs). The existence of these distinct regions provides ILs with the ability to solvate both polar and nonpolar molecules and has important implications for applications such as energy storage, nanoparticle growth, biomass processing, and organic synthesis. It has been found by computational studies and x-ray scattering that the morphology of the mesoscopic structure is highly sensitive to the alkyl chain length, however, the influence of aggregate formation and morphology on physicochemical properties, such as ionic conductivity and dynamics, is not yet well understood. In this study, a homologous series of imidazolium, quaternary ammonium and phosphonium-based ionic liquids are investigated by broadband dielectric and shear-mechanical spectroscopy as well as molecular dynamics simulations to elucidate the impact of alkyl chain length and hydrophobic aggregation on charge transport and dynamics. It is observed that systematic ordering of ionic liquids into complex polar and nonpolar domains results in the emergence of slow, sub-α dynamics in both the dielectric and shear-mechanical spectra. These findings confirm the existence of long-lived nanoscale aggregates in neat ionic liquids and provide a new avenue to elucidate the interplay of morphology, ion transport and dynamics in these nanostructured fluids.