Well, I think we all agree EPUB format is the king in the ebook kingdom, but FictionBook (FB2) is also a very popular format which many ereaders support, and, like EPUB and unlike others as MOBI or PRC, is an html/xml-based open and fully editable format, so I think it could be a good improvement to implement that feature to Atlantis.
Yes, Calibre can convert from EPUB to FB2, but it performs very badly, and, for instance, the EPUB TOC is always missing in the process. Given Atlantis' great ability to read and pass document TOCs to EPUB files, it would be very easy for it to do the same with FB2 files.
I'm conscious of Atlantis developer's reluctance to consider exporting to ebook formats other then EPUB, but even so I think maybe it could be worth considering that chance.