Alrighty, I'll take a shot Rafiki. (Or should we call you "Grafiki?"

)
Here's my proposal! Mileages are for mileage with a pack on, and distances taken from the mileage chart found on the forum. (Except for Lane Cove to McCargoe; the chart indicates 22.4, and it's probably 12.4..)
I didn't match it to ferry schedules, but I'm guessing you'll work that out...
Parameters: Arrive and Depart at Rock Harbor; allow for one intra-island ferry per trip; up to two weeks on Island per trip, strive for no more than 9 miles per day in first week of journey. (*That is more difficult on the West side, where camps are more distant, but I kept it close as possible.)
Trip 1:
1. Ferry to Rock Harbor. Day hike to Scoville point, get in those trails. Spend night at RH.
2. Voyageur II from RH to Malone. Get off ferry, begin the lovely hike up to Desor S. (10.8mi)
The first half is
fairly level and follows the lake, the second half to the tower is up, then you're good.
3. Desor South to Siskiwit Bay (9.9mi)
In the trees until Island Mine, and then down to the bay.
4. Siskiwit Bay to Feldtman. (10.2mi) Hike down to Rainbow Cove after setting up camp.
Up and over the ridge, but a
health day's hike.
5. Feldtman to Windigo/Washington Creek. (9.1mi)
Pretty typical Isle Royale for the next couple days..
6. Washington Creek to Hugginin. Take Eastern loop. (4.2mi) (Rest day)
7. Hugginin Cove to Island Mine. Take Western loop of Hugginin Trail. (10.0mi)
Sorry about the uphill, but it's not
horrible..
8. Island Mine to Hatchet. (12.8mi) (Your first official backtracking from Island Mine to Ishpeming Tower)
It's a
longer day, but you're up on the ridge for the most part, with not too much up and down at this stretch.
9. Hatchet to Chickenbone West. (7.9mi)
Yay! You get to go DOWN off the ridge, instead of the other way!
10. Chickenbone West to Daisy Farm. (7.9mi) Set camp and hike the "triangle" without packs, or at least to Tower and
back via Mt Ojibway Trail.
Classic Isle Royale Greenstone hiking.
11. Daisy Farm to Rock Harbor, cut over at Threemile and hike Tobin trail. (7.7mi) Catch Ferry off island.
The Tobin
Harbor trail is fast and easy. Just wake up early, depending on your boat.
Trip 2:
1. Ferry to Rock Harbor. Hike to Threemile. (2.7mi)
What an easy start!
2. Base at Threemile, presuming 'off peak' season. Dayhike to Hidden lake/Lookout Louise on Greenstone and back.
3. Threemile to Lane Cove. (4.6mi) Up and over.
Just try not to think about the return out of Lane Cove just yet.
4. Lane Cove to McCargoe Cove via East Chickenbone trail. (12.4mi)
As you indicate, it would be a long day, but take
your time.
5. McCargoe Cove to Todd Harbor. (6.6mi)
The easiest stretch of the Minong, IMHO.
6. Todd Harbor to Little Todd. (6.7mi)
Only one or two ugly water crossings, if water is high. Otherwise, a great
hike.
7. Little Todd to Desor North. (5.7mi)
A gorgeous section of trail, albeit slow, mainly because you need to watch foot placement.
8. Desor North to Washington Creek. (12.6mi)
Up/Down. Up/Down. Up/Down. Repeat. Like x18.
9. Take Voyageur II to Rock Harbor.
Set back and enjoy looking at the ridge you just crossed from the lake view!
10. Ferry to Mainland!