Basically you have to determine what group of people you want to target. Then you can assimilate what you want to do with the distro. As qub said, installing Gentoo (stage1) and LFS will give you a good idea of how Linux works on the inside. Then you can procede from there.
Ask yourselves questions like "Who do we want to target?" and "What would I want if I was our target audience?". I personally don't think that there is any distro that's lacking. You can find what you want in different distros. And if you can't, there's Gentoo, which is what you make it.
