Originally, eV might have been the right unit for electron energy used by people who were doing experiments with cathodic tubes. In those experiments, a cathode was emitting electrons if there was a cathode-anode bias. The multiples of eV are the right unit if you do accelerator physics. MeV, GeV, TeV are chosen because they are also closest to the order of magnitude of the electron energies in those accelerators. So, as a rule of thumb, one chooses the unit closest to the order of magnitude of the energy in the type of physical phenomenon of interest.
For example, if you do electron transport in nanostructures (like carbon nanotubes) you might want to use meV for energies, nm for distances, and fs for time. If you are interested in the band structure of solids, the best unit is eV, as the band gaps for insulators are usually a few eV's.
On the other hand, if you do engineering and you work mostly with macroscopic objects, you will work with SI units.