In my experience the iPad simply cannot compete with pen and paper for taking notes. Handwriting on the device is cumbersome (since you either have to mess around with a zoom box or can only write a few short lines per page, even with a stylus), and the virtual keyboard is too slow and cannot be used without looking (if you are a touch typist).
That said, I sometimes use an app to make limited notes in presentations or meetings. So far, Notability works best for me. I usually take notes as outlines (bullett style), and that is very easy to do with Notability. It can also record audio and makes it easy to quickly insert simple hand drawn figures in the notes.