I found the following comment particularly helpful:
"In FX format, the large size enables shooting with about 36.2 megapixels, while about 20.3 megapixels are used for the medium size, or maybe if you're taking snapshots you'll find you can get by with the small size, which is about 9 megapixels. Both the medium and small settings use data from the full extent of the 36.3-megapixel sensor optimally processed to a smaller size using EXPEED 3. Therefore, we suggest selecting medium or small for normal use and choosing large only for, say, group portraits or very high resolution landscape shots."
I didn't realize that the selection of small, medium or large size applied to the raw files as well as to the jpgs. If I understand this correctly, this provides you with a 20.3 mp camera if you choose to shoot in medium setting. For all of those who thought that 36mp was simply too much, they can shoot in medium for most of their shots, and only use "large" when they want all the detail you might get in a large landscape, for example.
This is a big deal, I think, and it is something I didn't understand before.