I also struggled with the duplication issues, and I think I've found a solution that's right for me - it's still pretty new so we'll see.
Because of the nature of my projects and the nature of my brain:
1) I often need my project support materials to carry out my NAs. (e.g. "Write to Bob re: Steve's feedback on proj X" requires a quick review of my notes on Steve's feedback.)
2) Over half the time I write a list of possible future actions as soon as I decide I want to do a certain project (or even before, when it's a S/M) I have to make this future actions list to get the ideas out of my head
3) After I complete an NA I nearly always need to refer to the project support materials to determine the new NA
4) I like to note the completed actions and the date in the project support materials (otherwise I may forget having taken that action and will repeat it)
One day I was reading this forum and someone said that they put NAs on paper, one action per paper, and kept all those papers in context folders, and that was their NA list - and a light went on for me. I still keep all the past and future actions in a manila folder with the other project support materials. Then I put a sticky note on the front of the folder with the Next Action for that project. I treat the stack of folders as my NA list, just like others treat a stack of paper that way. When I have a small project with only a few actions (as happens occasionally) so I don't have to make a future actions list of have any other support material, I simply make a temporary folder for that project, with nothing inside it, and a sticky note on the front.
I don't think this would work for everyone. I do nearly all of my work at my desk, with an occasional trip to a conference room 20 feet away, so having a Next Action list that is many inches thick is not really an issue. I would have to come up with something different if I had to carry an NA list with me.
Theoretically the stack of folders could also double as my projects list but I still keep a paper projects list. Since the project folders are always getting shuffled about it is useful to have that list in one place in one order. Plus it makes it easier for me to check things off during the weekly review.