I've seen a shockingly small amount of my own country but I would definitely recommend Skye (very beautiful) and you pass Eilean Donan Castle on the way. I also love the scenery around Glen Coe - I only drove through it for the first time last summer and it's spectacular.
City-wise, Edinburgh is much more interesting than Glasgow (although that's me being a bit biased). Glasgow has a lot of art museums but Edinburgh is stunning. It gets ridiculously busy during the Fringe Festival in August so unless you want to come specifically to see that I'd avoid that time. The whole city centre is also still in the process of being dug up for trams to be introduced (it's only taken about 6 years and they're still not bloody ready yet). Other than that I'll throw in a recommendation for my wee town, Linlithgow. If you're staying in Edinburgh and fancy a day trip it's only 20 minutes away by train. We've got a beautiful ruined palace where Mary Queen of Scots was born (in fact, Chanel just used it for one of their fashion shows a month or so ago) and it's just a lovely, historic little town.
Hope you enjoy your trip, don't forget your midgie repellant for the Highlands, plus a rain mac and a good strong brolly!!!