But I still have problems with pen and paper.
I like the ability to add to notes and change them. Professors sometimes meander about in lectures, and I sometimes want to reorganize the ideas they present.
You cannot search efficiently with paper. I have terrible hand writing on paper. Papers wrinkle and drive me crazy. I write slower than I type - and it's assumed (by professors) that people are typing so they teach at that speed (ppt doesn't help). Paper cannot be as easily shared as documents.
Treat the notes you took in class as a rough draft. After class, revise your notes into a final draft. This way you can reorganize the ideas, simplify example problems, and fix any spacing issues or spelling mistakes. This helps you learn the material since you are working with it while it is still fresh in your mind, and makes studying much easier in the future.
You can mix and match your pens and paper without any fear of interface problems - a pen bought a century ago in Germany will work with paper made next year in Argentina. You can even pick up a piece of paper that a different pen was using, and carry on adding to the content with whatever pen or pencil you've got in your pocket. It's a complete, self-contained information display system. I could hand a piece of paper I wrote on to someone from the other side of the world and they'd be able to use it.
Anything looking to replace pen and paper is going to have to be seriously amazing. I'm genuinely astounded that people choose to make notes with Microsoft word instead. The only advantage I can see to that is that you can change what you wrote later (if that is an advantage).