user_none, I'm glad to hear that this is high on your to-do list!
Out of curiosity, I just used eReader eBook Studio to take a look at the PML generated during the conversion process for an e-book that I'm currently reading. The soft scene breaks are of course invisible on my Sony Reader and Kindle, but in eBook Studio they are plainly visible as two blank lines, i.e. three hard returns between paragraphs (there is only one hard return separating most other paragraphs). Also, the paragraph immediately preceding each soft scene break is centered for some reason, with this attribute extending through the first of the two blank lines of each soft scene break. You mentioned that soft scene breaks are currently not supported for eReader input; pardon my ignorance, but does this mean that the PML file is generated at a stage prior to eReader input? Also, if I add an eReader PDB to Calibre and convert it first to EPUB and then to MOBI and possibly other formats, does Calibre always go back to the PMLZ to do each conversion? By the way, can you recommend a better application than eBook Studio for editing PML files?
idolse, the earlier versions of eReader for Windows, as well as the Palm OS versions, displayed the soft scene breaks I describe above as three asterisks, probably because the extra blank space would often go unnoticed on small screens. The eReader developers apparently agreed with you on soft scene breaks for e-books and decided to "harden" them for the devices in use back then. On the Kindle and other newer devices, though, I think soft scene breaks can work as well as they do in printed books. In many printed books as well as e-books there are added cues to signal a soft scene break. Sometimes a paragraph immediately following a soft scene break will be unindented while most or all other paragraphs are indented. I just checked one Kindle e-book against a printed version and found that both use this method (extra blank space followed by a non-indented paragraph). I have also noticed in printed books that soft scene breaks that occur between pages are sometimes very easy to miss unless you're aware of the change in indentation, so it seems to me that the issue really isn't that different for e-books, except of course that e-books are reflowable and therefore a specific break may be more or less conspicuous depending on the device, font size settings, etc.