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Dude,
Don't blame Calibre for that. Your source is junk. Calibre is NOT an ePub editor, it's a format converter and library manager. It is AWESOME at what it does, but it's not going to use human-intelligence to smartly lay out XHTML and CSS in a simple, elegant and consistent way.
It very cleverly does "good-enough" conversions for use in a casual manner -- and it is highly dependent on a good input source; garbage-in-garbage-out is a law of the universe. If you want beautiful books and elegant code you have to add that value.
Start from scratch with either simple HTML or a very good TXT and mark it up yourself, either in a text editor (go NoteTab or go home) or in Sigil, or one of the other ePub editors (Jutoh, Atlantis).
I recommend that you not trash Calibre for doing a very good job of making visually presentable ebooks, even if it uses complex and redundant XHTML and CSS. It's doing the best it can, (the very best, actually, of any program out there) in a way that is effective across an enormous number of use cases.
It is not a tool for professional or artistic work.
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