The wife and I went for ~17 days this spring. Our itinerary was Tokyo (6.5d), Lake Kawaguchi (1d), Kyoto (4d), Nara/Mt Koya (1d), Himeiji/Kurashiki (1d), and Osaka (3.5d)

Just for some general thoughts that we had on our itinerary that the OP might be able to pick through for their trip:
- We were a bit conflicted with the length of our stay in Tokyo. Our days were full and we did not see EVERYTHING on our list. Probably needed one, maybe two more days to do some more day trips (home-basing from Tokyo), see a baseball game, etc. However, by day 6, we were starting to get a little tired of the hustle and bustle of Tokyo.
- Should have spent more time around the Five Lake region around the base of Mt Fuji. We borrowed bikes and did a little bit of touring but we should have allocated a day or two more. Ideally, I would have liked to hike a little bit of Mt Fuji but we were out of climbing season and it was spectacular just seeing it as a backdrop throughout the region.
- Four days was pretty good for us in Kyoto, though another day or two would have been nice. Lots to see but we started to get “templed out”.
- Our Nara/Mt Koya day was rushed and we should have allocated more time and split it up. Really enjoyed Nara and feeding the deer. We stayed at a temple in Mt Koya. Interesting experience but somewhat pricey.
- Our Himeiji/Kurashiki day was also rushed. Himeiji Castle was interesting but looking back, we could have reallocated the time to something else. Kurashiki had a nice canal district area but again, in hindsight I think we should have reallocated our time to somewhere else. For us Kurashiki was more of a stop along the way versus an end point destination.
- Our time in Osaka was just right.

We wanted to visit another island somewhere (like Sapporo region) but it wasn’t feasible for us with the 2.5 weeks. We also initially tossed around Okinawa but again, time-wise it didn't make sense and it would have pushed our budget.
Hiroshima (and local day trips) was originally on the list but got nixed because it was a little far and we were already pushing our itinerary.

I'd recommend doing a search in the trip report forum as a starting point for building your own itinerary (in addition to buying a guide book of course) to get an idea of what others have experienced and what might fit with your likes. Also, here are a couple of other personal websites with trip reports that I came across when doing research for my itinerary:

http://www.johnharveyphoto.com/Japan/
http://gardkarlsen.com/