Keep an eye on the weather - head east if the lows are crashing in from the Atlantic, you'll just be wasting your time.
I don't like Skye - roads too busy and it's sold its arse to tourism. Limited time, first trip - you could do a lot worse than Mull, with a mainland stopover at something like Ben Cruachan or Arrochar if you fancy it. Alternatively, take the Fishnish ferry from Mull and detour up through Moidart/Ardnamurchan, which'll be getting quiet by then. My sister had her husband do trips like you're planning and, having been to Islay, Mull, the Far NW, the Outer Hebrides, etc, her favourite was Mull.
Edited: 16/06/2012 at 03:05