Harry was robbed.
Considering that of all the senior officers, he was the
only one who didn't mess up in a major way at least once (thus getting the "I'm disappointed in you" speech from Janeway), he
should have been promoted.
Even if Janeway figured that it didn't matter since the Harry Kim she started out with died and the one she ended up with was from another universe, that still shouldn't have prevented her from giving him his due.