I like two-handed swords because of their higher attack speed, but I am thinking about switching to a war hammer to max out my overall damage output even further. If the war hammer's higher damage output is handicapped by its slower attack speed, though, it may be just as benficial to stick with my two-hander. At that point, it comes down to the subject of "play style" which is really more about what you think makes your character look cooler and a lot less about raw, objective numbers over aesthetic appeal.
I guess what I really want is a DPS chart for weapon types, but I can't seem to locate such a thing. Does a warhammer have a higher DPS than a greatsword or does its slow swing handicap its DPS to the greatsword level? It'd make sense if it did actually have a higher DPS. Since warhammers have a slower attack speed, the implications of missing your target would be much greater since it takes longer to swing, whereas a greatsword with a lower DPS would yield less damage, but better recovery of lost damage inflicted if you missed your target. Therefore, giving a warhammer a higher DPS would essentially make it the weapon of choice for players who have become better at coordinating their attacks while the greatsword would be the preferred choice for the novice since they can recover lost inflicted damage by being able to bust out another quick swing if they miss on the first try.
Best Answer
Here's a small exmaple of how DPS works in Skyrim. The DPS if smithed row shows how DPS will change if all weapons get the same smithing bonus damage of 46 (smithing gives a flat increase to damage instead of scaling to base damage)
As you can see, the weapons are more or less balanced without smithing, but with smithing speed wins over base damage every time. I'd recommend one-handed weapons unless you're not interested in smithing or not obsessed with having the biggest numbers.