We are going to be visiting Skye for just a couple of days. What should we do?
Well, that depends on so many things - weather, fitness, interests, etc. - that it becomes unanswerable as a general question. Come for a couple of weeks instead. Even then, you'll only scrape the surface.
Alexander Smith, in his 1865 classic, 'A Summer in Skye', said, "To visit Skye is to make a progress into the dark backward and abysm of time. You turn your back on the present, and walk into antiquity. You see everything in the light of Ossian, as in the light of a mournful sunset."
That about sums it up. You can never 'do' Skye in the way you might 'do' Rome or Paris. You feel it instead.