I can stay remarkably focused in a creative activity while away from a computer. Programs take more time from me by adding inconsistent friction to what I want to express, and spending time undoing the magic but wrong assumptions that are automatically applied break the flow for me.
This approach to describing interactivity flows on paper https://vimeo.com/133046716
Middlemanapp + scss + susy grids one for an html prototype which then becomes the style guide.
The great thing about software (and I definitely do include interactive/UIish stuff here...) is that the barrier to entry is pretty low. No need to do anything special just because you’re “prototyping”.