shields block more damage, plus lets look at the perks that shields specifically benefit from. the elemental resistance +50% when blocking, dragon breaths become ridiculously puny, especially with the common enchanted shields that already have frost or fire resistances. being able to run while blocking makes you more than capable of closing the distance with mages with minimal damage and without shouting. plus you get to knock them down then pummel them after reaching them. applies to giants also i hear.
two handed weapons deal more damage, but dont block as effeciently or recieve as many benefits from the block tree. you do gain the sweep perk though, hitting multiple enemies at once, but only in front of you, useless for one on one, but good when you are skilled enough to line up the enemies in a row in front of you. two handed weapons stagger more often than one handed weapons, but i would still prefer to have some defense in there.
to put it into MMO terms, (which i dont know much but i know enough), two handers are the spikers, they arent effecient at protecting themselves but they can deal a lot of damage quickly. onehanded/boards are the tanks. can take a lot more punishment while still killing the enemy, albeit a bit slower.