The main disadvantage I think many GTD apps have is that they focus on organizing information rather than helping users process it in accordance with the GTD workflow. I ended up designing my own GTD app for the mac as a result of my own frustrations. The advantage it affords me and others is that it focuses more on "process" and coaching users through GTD. Check out the sub-section in the backstory I wrote about it here called "The Downside of Lists and the Power of One At-A-Time."
The RSD Backstory