The conventional whiteboard is big and tactile, but has only two operations:
In practice, the difficulty in rearrangement deters the participants from undertaking the crucial activity of rearranging, or limits them to doing it in their heads, where no-one else can see and participate.Even if you try to make use of the whiteboard for serious visual thinking, eventually you tend to end up with something rather messy:
So if you know what you want to write, a whiteboard is great, but it is of limited use in exploring ideas by playing with the arrangement.
bCisive (desktop and Online) and Rationale let you move around boxes at will, without the constant rubbing out and rewriting.
Butchers paper is even worse than a whiteboard (you can't rub out), and sticky notes allow rearrangement, but tend to be too small for group use and are poor at showing relationships (the lines connecting the boxes).
So while manual tools are flexible and have several advantages -- cheap, flexible, tactile, easy to get started (at first) -- they are cumbersome when it comes to the rearrangement needed to uncover structure and relationship.