I also tried Calibre, but none of the programs did exactly what I had in mind.
Both Calibre and Stanza will convert Pages PDF files to ePUB. However, as you noted, your results may not be what you expect. Using these applications it is better to create a very simple PDF source file for conversion. While Calibre retains your images while Stanza drops the completely (except possible for the first one which it may interpret as a a book cover) and neither application will retain things like "shapes" used as sub-chapter dividers, text boxes/background colors, paragraph borders/rules, etc. If drop shadows are used, Calibre will simply render them as black rectangles. Both applications may do strange things with text depending on whether you use blank lines to separate paragraphs and or want paragraph indents, justified text, and such. Stanza also annoys me because it adds any header to the last paragraph of text on each page which adds an extra carriage return and divides the paragraph into two parts. For these and other reasons, I have switched to custom Pages PDF files targeted at 800x600 displays at 180 DPI. This allows me to create a single file for use on both my Amazon Kindle 2 (800x600 @166 DPI) and a Sony Pocketbook Edition (800x600 @ 200 DPI). Since I only create files for my own use or reading to the grandchildren (i.e., what I call "personal publishing"), this "non-print" work flow serves my purpose but may not be suitable for you.
I'll have to look more closely at InDesign... I have CS4 but am not familiar with its ePub features.
The basic strategy here is to create individual chapter documents and save them. You then create a "book" project and assemble the saved files to it. I tried the free 30-day trial software be never managed to create a good ePUB file. InDesign is great for layouts but its "in-line" handling of images seems less functional than that of Pages' -- especially if you want to include a captioned, inline image. (I.e., you have to clipboard and group the image and text rather than simply creating single texted image object as in Pages.)
In any case, good luck. After looking at the currently available software, I opted to stick with Pages for ease of creating files which are, for the most part, compatible with both of my readers.
