Hi Stephen,
you're right, the new features aren't complete, I decided to release this version early because I'm working on another project and it would have taken too long before finishing. It seemed to me enough powerful to be released as is, but it will be improved in the future.

The black lines are there to "outline" things?

Yes, the black lines are needed to help the user distinguish the objects, especially walls. For example if you look at the last picture I've posted you will see that the house is L shaped, but when viewed from the side ("front" and "left") in parallel projection the walls that are parallel are exactly of the same color, and there is no mean to distinguish them, apart from the black edges.

Unfortunately the full geometry being outlined makes it a bit ugly.The lines should only be drawn on a) where two faces angle is greater than "x" or b) a material change (maybe?)

I agree with you, but I think it would be too complicated to implement this in a plugin. I will think about it, but I don't know if and when it would happens.

the horizon in black behind the building is ugly

I agree again. This happens because the ground has no thickness and becomes invisible when viewed from the side, the black is just the default background normally hidden by the ground. I have to find a workaround.

just make the entire background transparent or flat white

That's my intent!

About navigation
You're right again, I forgot to talk about it. Of course in parallel projection the size of the objects shown doesn't depend by the distance from the observer. To workaround this, I have introduced a new parameter named "parallelScale", but let's call it "zoom" for simplicity. However the camera position isn't meaningless, because it still affects which object are shown (objects behind the camera are hidden). So there was the need to control both the camera position and the zoom, hence the introduction of a new key modifier for the mouse scroll wheel: the CTRL key. If you hold CTRL, then the wheel will control the zoom, otherwise it will move the camera back and forth as always.

Another oddity I found playing with this is getting pictures out of SH3D. The parallel projection does not get used in the "Create photo" dialog. It defaults back to a perspective view, so getting a nice big high res image of a plan, elevation or section is not really possible.

I know, unfortunately it would be too complicated to hack the photo creation tool from the plugin. Maybe in the future.

the lines are rendered in the two lower quality modes, but they are too thin causing them to become broken into dots and dashes if that makes sense. So it'd be nice to be able to configure that thickness.

Oh, I didn't check this. I don't know if it could be useful without the parallel projection, but I will check if it is feasible.

Lines are not shown in either Yafaray or Sunflow renderers

I really fear the outline cannot be implemented using photorealistic renderers, it wouldn't be, how to say... realistic

Many thanks for your feedback and stay tuned for updates!