Thanks for the suggestion - it's an interesting thread.
I've found doing conversions in general to increase the labor required to get what you want to do in the first place! (For example, when you OCR a document, even if it's 99% accurate, the remaining 1% on a large document can amount to soul-destroying/time-consuming manual corrections).

Ultimately, it seems that PDF isn't an easily manipulatable format. The bluebeam PDF Revu I referred to is probably one of the most sophisticated pieces of windows based software for pdf manipulation, and yet I still found it to be hassle. But then again I'm expecting it to seemlessly mimick the workflow of marking up a paper pdf.

I doubt the Edge can improve on the feature-set/usuability of something like PDF Revu, but it needs to improve on its current usuability if academics are going to take it up for serious use regarding pdf annotation.