Two-handed axes are generally better. Even with 5 blacksmithing their minimum damage should always be lower (It's been consistent all the way up to level 15 like that for me). Now given the lower min damage and higher max damage their average damage is often the same until you take into account criticals.
A crafted two-handed axe can get +crit chance which is far better than anything a two-handed sword could get. I believe twohanded axes in the world are likely to have the same thing.
Onehanded swords and axes are much more imbalanced though. Onehanded axes always have the same minimum damage as one handed swords. Onehanded axes always have higher maximum damage than onehanded swords. Onehanded axes have 2x crit multiplier versus sword's 1.5x. Onehanded axes have superior bonus at blacksmithing 5 versus onehanded swords.
