My wife and I stayed 4 days in Fort William and hiked and spent 4 days on Skye and hiked and loved both areas. This is a tough call. I particularly enjoyed the Glen Coe area for hiking while staying at Ft. William but we visited the viaduct to see the train chug thru at Glenfinnen and it ws great and we hike around Ben Nevis, but not up the mountain itself due to time and old legs (60's couple). I had put the hike up Ben Nevis for our last day and after doing Glen Coe area hikes and others we did an easier hike the last day.. We had a great B&B just south of Ft. William, Hunting Tower Lodge. Food in area was great!
But, if I was only choosing one spot I would do Skye. We did several hikes in the Trotternish Penns. area and down around Carbost, where our B&B ws located. If I return (I hope to) I would spend a week on Skye. The hikes were varied for what you see and how difficult you want them to be, we had blast on Skye. Things are spread out a bit and the night life where we were was hard to get to (pubs were great though) so you have to plan your evening meals to be able to hike, rest, eat/drink.
http://www.blabheinn.scot/ These folks were great for our B&B on Skye, give them a look.
I based most all of our hikes and where we chose to visit by using the walkhighlands web site and the book those folks put out regarding hikes. It was a great resource and after I spent time getting familiar with it I used it for directions, hiking ideas, and planning. We also found the Ordnance Survey maps for Skye a must have for driving on the isle. I envy your trip!
Dave, Bedford, Indiana