I'm glad that there's so much discussion cropping up in this thread; even if there isn't a complete consensus on any given topic, we can still refine our arguments and better share our experiences with the game and our perspectives on any given flaw or design choice. I've been a little busy as of late, but I'm definitely keeping my eyes peeled for suggestions and criticisms.
The only thing I'd like to clarify is that the Systemic/Major/Lesser categorization is less about showing the importance of an issue and more about describing its impact on the overall design and experience, and its relation to other flaws/design choices. A systemic issue is one that has deep and numerous effects throughout the game, a major issue is closely tied to other issues or has a noticeable presence in the game, and a lesser issue is a relatively independent problem or underdeveloped aspect of the game.
This categorization is also the most subjective feature of the document, but I felt it was a good alternative than trying to objectively categorize the importance of every issue, as opposed to trying to judge its overall impact.