I'm a developer with crocodoc. Thanks, that's what we're trying to do! Would you mind sharing the details of your painpoint? Feel free to email if you would prefer not to reply publicly, my email address is in my HN profile.

It sounds derivative, but in fact crocodoc is great. While there are lots of document markup tools, I actually use and like crocodoc. Use it a few times to mark up a real document and you'll see.