Sorry to necro this thread, but I've ran into the same workflow issue as Jenna, had to switch to a more heavyweight app in the end.
Given that paint.net already has brush hardness, it should be trivial to add opacity (scale hardness function) I think, which would make the paint tools more powerful.
I wouldn't even mind to contribute (code-wise) if there was a way.
Here a quick and dirty mock-up of what I mean: