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Why? Unlike with the regular distributions out there, they are essentially in control. They decide for you what the bootscripts look like, they decide for you which directory layout to use, they also decide for you how packages are compiled (which options enabled by default, which not). Then they decide where programs store their config files and how and for how long.
There's not a whole lot that you have total control over. Linux From Scratch is different in that regard. It lets you build your own Linux system from scratch. Get the source code and compile it all yourself, manually. Added bonus: you learn a tremendous amount how Linux systems work behind the scenes, what all those hundreds of files are for, which ones you really need, which ones you can safely remove, a bootscript setup according to your requirements, and the list goes on.
You should try to ask this type of question in the Distribution forum and you should be able to setup a poll, but you should go ahead and check out the Members Choice Awards as people are already voting for the best Distro for the year.
I would have to agree with lfslinux, LFS is a great solution if using Linux. But my personal favorite of choice that you don't build yourself would be Slackware, its the most unix like and I like to configure settings by hand, not gui interface which makes it easier to understand/learn...etc.
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