The pencil-case-as-cover idea for a Traveler's Notebook seems useful, but I think it only works if it lets you leave a separate pouch at home. If it just adds another layer around the notebook, you end up carrying the same supplies in a bulkier package. I like the appeal of keeping a pen close by, but the built-in case has to earn its place.
It needn't replace the whole pouch every time. If the built-in case holds my usual pen and pencil, the separate pouch can stay home on ordinary days and come along only when I need a fuller kit.