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1) Folder structure isn't very useful compared to collections.
Although there is a definite use for managing collections via the desktop. Speaking of which, have you seen Ixtab's Collections Manager (kindlet), or barsanuphe's LibrarianSync (KUAL extension)? They even integrate into calibre.
2) What exactly do you mean by that? Aren't you adjusting it to suit your needs right now, by turning off a feature you dislike?
3) Lots and lots of people successfully convert EPUB to AZW3 and preserver their fonts.
MOBI on the other hand does not support embedded fonts at all.
You can try our Fonts hack, or ask in the calibre forums why your fonts aren't converting, but I highly doubt Amazon would have gone to all the effort of developing the mobipocket formats if they were going to then ditch it for EPUB.
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