Say I have Motivation on Luke Skywalker. I exhaust it during his activation and later that turn play Son of Skywalker. Does Motivation get readied as well, or does it only get readied at the end of the turn?

The reason I ask is because I seem to remember from the campaign rules that a hero's abilities are all readied at the start of their activation, not the end of the turn and wonder if it is similar for Skirmish.

No. Son of Skywalker is pretty clear it only readies the deployment card.

Also, abilities that affect deployment cards do not work on skirmish upgrades unless explicitly stated so (see FAQ).