Its a dilemma that most people go through when deciding what tools to use for their productivity system (whatever flavour that might be). Some systems force you to use a particular format (which takes the decision away, but invariably means that the system could lack flexibility and customization).
This article suggests using a similar system to myself - USE BOTH. I like the quickness and spontaneity that a freeform piece of paper gives, but anything that happens on that piece of paper get condensed and fed into my electronic system at a later date to allow for archiving. The paper is just short term storage. A piece of paper also doesn't remind you of that meeting that was booked a fortnight ago that you need to travel to.
Each media has its benefits, so why not use both!! There are of course more unusual ways of using both systems at the same time.
[Paper vs Digital Debate... at LifeDev]