I am biased but would definitely include Skye which in a way distills much that Scotland has to offer into a relatively small area; mountains,, lochs, coast, historic buildings, whisky distilleries etc etc.
The drive to Skye is pretty awesome, too, assuming you are coming from the south; can include Loch Lomond, Glencoe and Glen Etive and Ranoch Moor before arriving at Fort William and the nearby Ben Nevis which is the UK's highest mountain.
Not sure of your budget but suspect the above courses are more than you might want to pay! You can easily arrange a trip yourself using budget accommodation such as hostels, bunkhouses or camping (although some sites may well have closed for the winter).
On Skye check out Elgol for it's coastal views across to the Cuillin mountains. Sligachan for old bridge and Cuillin views, also campsite and accommodation and the pub has a wide range of single malt whiskies. Neist Point for the lighthouse and sunsets. Old Man of Storr and the Quiraing.
Let me know if you want any more details. I may well be on Skye etc for some of October so may be able to help point out things.
Enjoy your trip. The one big down ide of Scotland, midges, should be long gone and with a bit of luck you may get some good weather but don't bank on it.
