I don't know of
any software that can completely edit content in PDF files. Acrobat allows some manipulation, but not really editing, and Illustrator can open a page and allow some modification, but it's limited. PDF is pretty much a one way street in this sense.
The one semi-exception is that Illustrator can save an 'editable' PDF file, but what this is actually doing is to embed the actual original Illustrator.ai file in the PDF as a payload attachment, which Illustrator can later use for 'editing' the PDF.
It might be useful to have Prince attach the original HTML and CSS source code in the document, and although I can't think of a demonstrably useful real-world scenario for that right now, I'm sure someone can.
Note that this is all quite different from a Tagged PDF, which is something else, and seems to be on the radar:
http://www.princexml.com/bb/viewtopic.php?t=102