Bones is the only real exclusion from the album in terms of singles. Personally, I'm sort of glad that it isn't a complete representation of every one of their singles though. Things like Jenny Was a Friend of Mine and or the Sawdust singles (Shadowplay and Tranquilize) can still be discovered after buying the other albums, you know?
I'm sort of happy The Way It Was was included as the "non-single" for the album, probably due to its reception during the live shows this past year. Considering that Here With Me didn't do anything chart-wise, I don't think it's too big of a loss there.