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The trouble with plain text is it lacks the necessary 'expressibility'. Even for fiction, you occasionally need to emphasise words or clarify/distinguish blocks of text (eg for a change of tense or perspective, etc).
For online viewing, I think HTML is suitable for most purposes. The biggest drawback, however, from a publisher's point of view, is the lack of DRM. The absence of file compression and 'packaging' can also be a nuisance.
For documents that will be printed, PDF is probably the best bet. Again, the biggest drawback from a publisher's point of view is the lack of decent DRM.
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