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Anyway, I don't really get the comment about customization. It sounds like you're looking for a DTP program like InDesign rather than a typesetter like TeX.
You're probably right but I just want to be able to customize my thesis the same I could do it with xml+css. I think it's much more flexible than LaTex. Maybe it's just something else than typesetting, but LaTex is also supposed to do some customization with all these packages but I feel it's a bit outdated for this.
True separation from contents and style is easier to achieve with xml based languages. Like tbook for content, css for style and fop for typesetting would seem to be a nice alternative.
But I agree that for now there are no valid alternative.
I also know that customization is really not important in a thesis and has to be used with caution but I am a perfectionist ;-)