I totally agree with you, it's very complex, heavy loaded and not lean at all.
There is an "alternative" in the marketplace that might fit your needs:
Hi Kitti,
I have implemented the questionnaire module twice now and my conclusion is that I wont be using it again.
Both implementations required custom changes to the module which took a significant effort. Unless you are able to use the module straight out of the box, I would recommend starting from scratch.
From your description of your use case, it sounds like a wizard integrated into a small workflow may work for you.