What appealed to me was that there are probably enough differences between the islands for survival to take very different forms from island to island. It would be an area where you could run something akin to a "Free Trader" campaign (a la Traveller) using a Puffer (I also found an interesting ship based in Rosyth in the 1990's that a GM could get going again -
http://www.maritimesteamrestorationt...l_history.html ) or some other vessel.
Although canon says HMG have abandoned Scotland you could well have some units left up there. There were RAF personnel at several of the RAF bases on the West Coast (obviously) but also Royal Marines and US Navy Seals at Machrihanish - indeed you could have something more exotic up there if you wished:
http://www.dreamlandresort.com/black...hrihanish.html
I think Islay could come out pretty well - they already have arable farming, ample stocks of Scotch that would be a useful trade good (and obviously ample stills for production of fuel) and some fishing boats. The climate there is relatively favourable thanks to the Gulf Stream - it wouldn't be paradise but better than most places.
Other islands could be much harsher - and I think anywhere on the mainland would have a huge influx of refugees to contend with. I think Oban and Ullapool could be pretty rough places to live. And I've alway found Glencoe pretty creepy even on the sunniest of days (never trust a Campbell!). On the other hand some of those Scottish peninsulas are pretty isolated today so you would need to be a pretty determined refugee to make it all the way out to some parts of the coast.
Re Fort William - I would think that both Fort William and Inverness would become pretty strategic places to control as holding them would mean that small vessels could transit the Caledonian Canal - you could have waterborne operations on Loch Ness patrolling for marauders etc.