First, you don't have to live with Unity if you don't like it - you can choose to start from any of the variants: Kubuntu, Xubuntu, Lubuntu... but you could jus

First, you don't have to live with Unity if you don't like it - you can choose to start from any of the variants: Kubuntu, Xubuntu, Lubuntu... but you could just use the stripped down ubuntu-server distro, maybe change the default kernel and add a DE/whatever on top of that. Another option would be oem-config, which lets you customise repositories & packages, and end up with an installed system which can then be remastered (by means of rsyncing or by copying whole partitions) before the final user customisation. Ubuntu builder was a nice project too, it's a pity it was abandoned. Someone should definitely resurrect it! Edit: I re-read your comment and understand you're not talking about packages, but rather about actual package contents, paths, init system and the likes. Yes, Ubuntu (and to a lesser degree Debian) has its own ways; it makes no sense to try to undo their customisations - unless you have the power to write your own.