Some people say writing is better because typing is "unnatural", but from an evolutionary standpoint both are extremely, equally unnatural activities. There's no reason moving a cylinder of graphite with one hand should be inherently better matched to the brain than moving squares of plastic with two.

My personal guess is that, with fast typing speeds, it's too easy to just copy things word for word. With writing, you have to at least rephrase it and reorganize it to fit the notes reasonably on the page, which forces some processing to occur. I take notes solely by typing, but I only have retention if I do it slowly and reflectively.