Maybe the solution is that against an unarmored person, the daedric and iron warhammers do somewhat similar damage (the daedric will do more, but not vastly more). Then against armored people, the daedric one would do much more damage and wear out slower because it is designed for taking out armored foes, and the iron can't do as well against stronger defense materials like mithril.
That would be a good solution, but seeing as how they said maces get armour piercing perks, I think warhammers are only going to pierce armour with perks. Unless, they give warhammers innate armour piercing that stacks with perks, so you can bypass armour with less perks.
Well, the thing is, they are adding perks to handedness. This means they can keep the damage the same as Oblivion, but the perks can really improve the effect. For example, if two handed weapons inflict increased bleeding and possible stun, there can be a pretty good incentive to use it. Also, I think they should make some effects exclusive to handedness. For example, if stun/paralysis can only be inflicted by Shield and Two-handed weapons, I would certainly consider specializing in two-handed weapons. However, if every type of weapon can stun (like in oblivion), then the effect becomes stale.
I'm not really clear about the perk thing. So far, I know that swords can do more criticals, axes can cause bleeding and maces can penetrate armour, but are those only for one-handed weapons or also for two-handed weapons? If one-handed axes cause a bleeding effect of, say -3hp for 10s, and two-handed axes do the same, I would think that two-handed weapons are underpowered when compared to one-handed weapons.
Having a stunning ability would be good though, but it should be better than any the shield can do, because overall I think two-handed weapons should give the highest offensive capability, while one-handed weapons should give the most flexibility/speed, with shields providing the best defense.
Id rather have two handed weapons have another attraction along with more damage, though i cannot think of any, maybe greater knock-back/staggering/lesser penalties for hitting an enemie's block?
I think two-handed weapons should have increased damage and perhaps perks that are different from their one-handed counterparts, so while a one-handed sword has a perk that gives more critical chance/damage, a claymore could have a perk that gives more critical chance/damage while giving a chance for disarming opponents blocking with smaller weapons.