i don't have any experience with InDesign, but I'm a little surprised it doesn't convert ePubs out of the box.
The real problem with trying to convert linked endnotes to real footnotes is that endnote/footnotes are not "semantically" encoded in HTML/ePub; there's no technical difference between them and other internal hyperlinks, and so the converter would have to use some kind of artificial intelligence to tell what counts as what. Maybe just any link that contains only numbers and punctuation would count as a footnote? But even, it would have to guess where the linked-to footnote text "ends"--again, not an easy thing to code.
The footnotes/endnotes issue aside...
Personally, I think the output of Prince XML is quite nice looking -- definitely qualifies as "decent". And you can make use of
Jellby's wonderful script to automate the conversion process.
Ahi (a member here) was working on an HTML (and ultimately) ePub > LaTeX converter script specifically designed for ebooks, and personally I think pdfLaTeX output is just as nice looking as InDesign output -- in fact, I can barely distinguish them. I don't know whether he's finished it, and whether or not he's tried to deal with footnote recognition. If not, then there are other general purpose HTML>LaTeX conversion scripts out there you can try. Personally, I'd much prefer to see a polished ePub > LaTeXed PDF script than anything for InDesign, mainly because I don't have the money for the latter, but also, since pdflatex can be run from the commandline, it would make automation/scripting easier.