I've had this experience as well doing research. GTD is great for doing many small tasks that are hard to remember, but I always seem to have tasks that are hard to break up. Something like "Make machine learning method X work for data Y". Sure there are lots of mechanical things like importing/exporting data that are easily tracked GTD style, but then there is the core problem, that is very difficult to break up ahead of time.
I'm in a similar boat, and I also often find that figuring out what the larger task needs to be broken up in to is part of the process. I don't know all the steps until I'm partway through the process in the first place.
This is similar to a problem I have delegating tasks. Not always, but often by the time I detail out things that need to be done, and how to do them, for someone else with less experience, I could have just done the work faster. In the short term this is incredibly frustrating, and I balance that out by telling myself that over the long haul, getting others up to my level on certain tasks will mean I don't have to do it at all. But determining when to delegate and when to do, with real world deadlines involved, is stressful.
