It depends on what type of character you're playing. In general, I'd say one-handed is superior due to its versatility, speed, and ability to dual wield/cast. But if you're going for a "hulk smash!" type of character, then two-handed, and with a high heavy armor skill of course, reigns supreme. I personally think being strong in both skills is the best. I'm playing an orcish warrior right now and I alternate constantly between bow, warhammer, and war axe w/ shield, which allows many attack/defense options and provides a variety of weaponry that makes the game more interesting.
Attacking a bandit fort for instance: launch a few arrows taking some bandits out until a few other attackers get too close, break them down quickly with your warhammer, advance on the fort with your one-handed weapon or spell and shield raised (doing this with the Deflect Arrows, Elemental Protection, and Block Runner perks is optimal), blocking attacks until you're close enough to slice the remaining exterior defenders up, then go inside and wreak close-quarter havoc with your hammer or dual wield (especially with the Sweep Attack or Dual Flurry, respectively).
Two-handed is devastating everywhere and even more so with the Great Critical Charge perk (very useful in taking out Master Mages in one quick move), as well as when used on dragons; I can usually kill one the first or second time it lands. One-handed affords you a lot of crucial protection and versatility. Overall, a warrior should effectively utilize block and both one/two-hand skills (archery's a good idea as well) and all other character types are probably better off with one-handed. Hope that helps you out a bit.