Donphan, with his single ground typing is weak to water. A low level Vaporeon will easily take him out. His movesets also don't provide type coverage.
Also, Vaporeon also has higher max CP, and IV for IV, Vaporeon will sit higher than Donphan in gyms. In other words if you evolve your low IV Don its CP will be too low for gyms as a regular iV Vape at the same level can climb above it.
That said I like using my T/EQ Don once in a while as a generalist attacker, it's fun for a change.