From: Federal Way, WA
If you're going to Japan, I would save the smaller islands for another trip. Transportation in the region isn't exactly like what we're used to in the "First World."
You could easily spend the whole 3 weeks in Japan, and there are plenty of things worth seeing. Two recommendations that haven't come up, yet:
1. Nagasaki. The Old Dutch Quarter is fascinating, and the Peace Park is, well, peaceful. One of the best experiences of my life took place there when a Japanese gentleman wanted to take a picture of his family with the Americans.
2. Nagoya. I haven't checked lately so things easily may have changed since I was there in 1985, but there was no airport departure tax so that's where we left to return to Guam. In Nagoya, be sure to visit the Noritake China factory.
Speaking of Guam, that -- and Saipan -- would be my places to tag onto the end of a Japan trip. Almost nothing to do on Saipan but relax for a couple days, though you can see some of the WW II sites there -- they also have a fantastic botanical garden. You'll use up the attractions in 2 days. Guam, of course, is still 50% (at least) military and is no longer what it was in the 80s -- think Hawaii of the 80s and you have Guam (that's pretty consistent over the years; Guam is about 30 years behind Hawaii in terms of development). Lots of historical sites along with the friendliest people on earth. If you happen into a village while they're holding a fiesta, which means almost any weekend, you'll be more than welcome to join in. Lots of natural beauty, as well -- the Pools of Inarajan and Talofofo Falls are recommended (although the latter now has an admission fee).
Plan a separate visit another time to visit the SW Pacific islands. Air service is rarely on a daily basis though, on the bright side, it tends to travel between the places you'd want to see (Honiara, Tarawa, Nauru...).