When a regular skeleton is holding a sword, it's damage is always 2 (normal difficulty). It is not affected by the weapon type.
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I got annoyed by this as well. If you're a mapmaker, a workaround is to give their swords the Sharpness enchantment, but bear in mind after a fix you'll have skeletons stronger than you intended 😛
Confirmed, on Hard, a Skeleton with a Diamond Sword only did about 2 hearts of damage, where as a Zombie will do their melee damage + sword damage based on difficulty.