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i don't know much about fan fiction so i can't address most of your points, but since you brought up formats, yes, mobipocket is a very commonly used format at this time, and epub is the emerging industry standard. as you say it is open source and a very robust format specifically for books. in addition, it can easily be converted to other format (like mobi). it's an excellent format to create because it will allow for very good formatting, meta data and archiving, and converting it to other formats as needed is trivial.
you make some very good points about exploiting the new technology in fan fiction as other media have done and i think you've got some very good ideas and it's an excellent initiative.
good luck with your endeavour.
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