I like the new look and functionality.
Two first blush comments:
1) On the report document, I can imagine my security officials freaking out over the in-your-face "The system is not compliant!" text. What is the recommended course to ensure this text does not appear if you're running the scan on a webserver, for example? Is it as simple as creating a custom profile derived from the STIG profile? Does anyone directly use the STIG profile, have a completely compliant system, and have a server that actually does anything useful?
Up to now, I've left tests in that I have waivers for, and then pointed at the waivers to justify the test failures. Perhaps I will need to change that practice.
2) On the guide document, the text beginning "Providing system administrators" occurs twice.