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Calibre does not produce good FB2 files - I've examined a few manually and there is markup that just doesn't make sense. Lumps of text not surrounded by <p></p> where the context clearly indicates that it is part of a paragraph is just one example. To be fair FB2 is a new format for Calibre and it probably needs a bit of work.
As far as size goes I don't think it is a "format" issue as such. Using stock Hanlin software with Coolreadre as the FB2 parser I have some large FB2s that bomb out and others, larger, that display o.k (albeit very slow to respond). I think, though, that it's fair to say that FB2 is not ideal for large files.
BobC
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