The most crucial distinction where paper wins is that writing is a "nonlinear" process whereas typing with the tools we have today is "linear". You could use something like a mindmapping tool, but you're again constrained to a fairly rigid format rather than giving you the ease of switching. Eg: you can write down a bunch of things and draw arrows between them. Or draw a graph/sketch. Or draw a link between the thing…
> I can think while I write, but not while I type // To me handwriting is more rigid in that one can't rearrange thoughts without drawing big arrows and having lots of crossings out. But then I only type and don't hand-write so perhaps I've lost track of what I'm missing out on. Do you touch type? I don't by the strictest definition but I don't look at the keyboard and can have a conversation whilst typing - I'm not…
I think a major part of handwritten notes is that it does force you to select what you're actually going to write down, and that is an inherently synthetic activity. Synthetic activities lead to more effective memory formation.