My thoughts on this is there is a deliberate act going on that is doing more for retention than just the simple act of using a (fountain) pen.

If I am in a lecture and I am writing down everything I hear as fast as possible in one ear, on paper, out the other style I don't think writing is any different than typing the same way.

If I am in lecture and I am trying to stay deliberately between the lines of paper, then I have to take the info in, process it in a way where I analyze and summarize it, and then put it on paper neatly. I have to do that for brevity and to keep up with the lecture. Its not the act of just writing, its the analyzation that occurs before the words hit the paper. This can be achieved with typing as well if you deliberately style your notes.

I think sometimes we correlate this in too simple of terms to use pen = better, the pen forces the deliberate action of analysis easier than typing does.