I'm biased, I'd scream Shetland all the way when it comes to Orkney and Shetland, but I have spent a bit of time in Orkney as well and its a pretty good place to go if your looking for the cultural edge in easy to find sectors, by comparison Shetland is just as good, but you have to go looking for a lot of the sites yourself as we've not been quite as Historic Scotlandised as Orkney has, not saying its a bad thing Historic Scotland have done a lot of good work in the conservation of historic sites, its just not to my tastes and Shetland is to all intents a purposes a lot wilder than Orkney. The boat north from Aberdeen takes 14 hours, if you go for a cabin its expensive, if you go on as a foot passenger and are willing to sleep where you sit, then its really not that bad especially if you take your own food, and theres a couple of bars on board where you can get a drink and plan what you want to do. But Shetland is about 80 miles in length, and as Copepod said you can be here for months and barely scrape the surface, and there is a mass of things to see and do. With that in mind I would probably suggest you hit Orkney this time and then come back and hit Shetland on its own to really experience what we have to offer.
August in Orkney, particularly Stromness, will be busy as there is an international sea angling competition going on so accommodation could be hard to come - by. Getting to Orkney from the highlands is a trip to Scrabster from where you can get the boat over to Stromness, its a short ferry journey and takes you around the Old Man of Hoy and around some of the highest sea cliffs in the UK. From Stromness its easy enough to get over to Kirkwall, visit Skara Brae, Stenness and other historic sites. In Thurso there are a good few bars, a tourist hostel and an almightily cheesey night club. Scrabster is largely just the harbour with the ferry terminal, fish market, ice house and lots of boats. There are 4 sea angling charter boats and 1 sailing and wildlife boat which operate from there.
From Skye to Ullapool take the coast road, having driven it 4 times now it doesn't get old and it is stunning. The from Ullapool head north towards Cape Wrath and Durness, head to Balnakeil for a great hot chocolate and then go east through Tongue and Betty Hill to Thurso and Scrabster from where you can get the ferry to Orkney, come back to Scrabster at the end of your trip and head down the A9 to Inverness through Latheron Wheel, Brora and Dornoch before heading south to Aviemore (all that in itself is enough for 2 weeks to be honest). As you are going to cover a really big area I suggest you get either a travel card for the trains or hire a car this will make things easier when your in the north west and it also gives you somewhere to sleep if no hostels are available. You can leave the car in Scrabster for the 3 days you are in Orkney as they have carparks specifically for that, there is a charge but its not a lot of money.
Enjoy your trip