Video here: http://vimeo.com/13108357 I recommend watching it first. This was a pretty emotional trip, and I don't care to try putting it into words yet. Ergo the visuals stand in that stead.
Some comments geared towards encouraging others to plan their own trip.
Firstly, do it! Go! Isle Royale is quite the unique experience. Getting there is a headache, takes some time and planning, and is expensive. The results are worth it. Over 90% of the annual visitors to Isle Royale are backpackers. About as many people backpack in Isle Royale in a given year as do in Yellowstone. The average visit to Isle Royale is four days, about 3.5 days longer than most parks people can drive to. It gives the places a vibe to be savored.
We (my parents, sister and I) flew in and out with Royale Air Service. Class act company. More expensive than the boat, but for four people to get to Rock Harbor then take the smaller ferry around to another TH, not as much as you might think. And it is much, much faster, You get to see the island from the air, and get another 1.5 days (effectively) to be on the trail. Just keep in mind that the likelyhood of fog delaying your flight in or out is not small. Our flight in was delayed two hours.
The landscape is totally unique in my experience. The island is glacier scoured along its long axis, and the trails going perpendicular to that end up hopping from micro-ridge to bog and back again. Plenty of very short but steep climbs, and lots of fun boardwalks.
Minong ridge rules! The westernmost 15 miles are the most difficult/rockiest/hardest to follow, but have great views, varied and cool terrain, and get you up in the breeze and bunch (and thus out of the bugs). That being said, the difficulty of the hiking and route finding on the Minong (based on the consensus found online) is somewhere between grossly to comically exaggerated. A big climb on the Minong is one that gains more than 100' vert, and while the trail can be faint for stretches, you'd have to try pretty hard to get very far from it. The trail climbs the crest of the SW side of each ridge, and tends to descend from the NE end between 70 and 50 yards from the end of each. When its in the woods the trail is dead easy to follow.
Great campsites. Lake Desor North and Todd Harbor were both superlative backcountry campsites. We had both to ourselves (one dead quiet neighbor out of sight at the former, no one at the later). McCargoe Cove is more likely to be crowded, but spent an long afternoon on a hot and sunny day swimming off the dock and lounging around before cooking dinner and hiking to E Chickenbone in the evening. E Chick isn't bad, but water is a longish walk away, and compared to others its a lackluster sight.
When I go back I'll follow the rule of trying to camp on the biggest body of water available. Better views and breezes are both welcome.
We seriously lucked out with our timing. Effectively no rain, never too hot, and shockingly few bugs. Locals told us an early thaw and cool spring had made it an atypical year for bugs, and we certainly could have been much worse off. The payoff for the gamble was being around for the height of wildflower season. The colors were stunning, everywhere.
My last thought is that carrying a heavy pack sucks. My parents aren't in good backpacking shape, and the only bugproof shelter we had for four was the 11 pound Sierra Designs Mondo Condo. I put that, most of the food, my packraft, and my normal light personal kit in a huge old Dana pack, and suffered. 15 miles felt long, which given my fitness and normal mileage on trips (often twice that, with less suffering) made the load just seem aburd. My hips were bruised by the end. Never again such a big pack. You can see the difference in my gait during a lot of the video segments, I'm plodding along like some cartoon yeti.
If you're a serious backpacker, you really need to go to Isle Royale, at least once.