You should be getting a vector result from the PDF export, have you tried that one yet? I just opened a Scapple-generated PDF up in Illustrator to check, and I could manipulate all of the lines freely.
I use Pixelmator in lieu, and no it didn’t work when I opened a PDF format. It opened as a rectangular object that I could only resize. The individual nodes however, well, I could not change their positions.
you guys have a fine raster integration (png, jpeg, etc) but I think proper vector integration needs to be done
Oh okay, I think Pixelmator is primarily a raster editing program, no (the name would certainly suggest so)? It’s been years since I looked at the demo for it, so I may be out of date, but your description sounds like how programs such as these handle opening PDF. It’s just a solid object that you can position and resize. But, in Illustrator I can go in and modify the bezier curves on the connector lines, if you want to tidy up a snarl of overlapping lines. I can change the way arrowheads look, anything. The whole thing is editable. Perhaps there is a free converter, or even vector editor, that would do a better job of opening it.