Hello,
  Yes, having projects in the agenda is annoying. I use the philosophy from http://doc.norang.ca/org-mode.html where any task with subtasks is a project. Stuck projects are those with no next action.

I have several projects which have many nested sub projects in them.

Prior to org mode, I tried so many apps to get this basic feature, but not many are this malleable and still easy to use.

Thanks and have a good day!
Bala
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http://balaramadurai.net