Wow, this exactly how I organize my thoughts, and I've been slowly thinking about the design of this tool too.
I think the most unsolved part is the layout of arrows. I've never used any drawing or flowcharting program that could connect items at the speed of thought. You always spend time fiddling with the pathing of connector lines.
The auto-OCR feature is tricky too. You don't want to waste time clicking the Rect tool to draw a rectangle.