I'm a doctoral student as well, been doing GTD for about 3 years now, and have been thinking some more about GTD & Academics. These are, of course, not limited to just academics and have overlaps with other types of jobs/occupations. Here's what I've discovered so far.

1. Academics Tend to Overestimate One-Step Actionables
Those who live and breathe and move in an academic environment are so used to doing the things they have to do everyday (e.g. writing papers, reading books, finding articles, studying in workgroups, etc.) that they often misjudge one-step actionables. Thus an academic is more likely to think of "Find a topic" as a one-step actionable with its next action as "@ Library: Next action to find a topic"; but the actionable is actually a more-than-one-step action (i.e. a project). There is more than one step and quite a bit more thinking that needs to go into this task which makes it a Project and not a one-step actionable. Hence there are many supposedly one-step actionables on an academic's next actions list that actually need to go to their Projects list for further brainstorming, outcome visioning, and breaking down into further actionables. I call them "actionable chunks." We can't do actionable chunks; we have to do actionable bits. And so the chunks have to be broken down into smaller bits in order for them to get done. So one way academics can move more efficiently in their GTD workflows is to reassess their action lists to see if they have overestimated items on that list. There may be some seemingly one-step actionables there that are really Projects that need to be broken down further. But because academics are so used to stumbling through actionable chunks -- like writing a research paper by forcing themselves headlong through the process -- it becomes really hard for them to break the bad habit of overestimating one-step actions.