Few people realise how much the simple act of writing efficiently - and taking notes especially, when you have to keep your attention focussed on something else - is affected by a myriad of small frictions and textures. Just try to write with a dull pencil or a ballpoint pen that's been in a drawer for 5 years.
If you're used to writing on paper, the apple pencil's hard tip on the iPad slippery (but due to fingerprints also suddenly less slippery in patches) surface might really be a new and mostly uncomfortable experience.
My advice would be to invest in a screen protector, but there are some caveats:
- if you get one of the "crystal clear" ones, the benefit would be to get rid of the unevenness of the original glass because it deals with fingerprints better, but it might still be too slippery and it will take some getting used to. The upside is that you basically keep a clear image;
- if you go with one of the many "paper-like" or "matte" ones, keep in mind you will see some rainbow effect on the white areas and the screen will look slightly blurred. If you use it from a distance the problem will be less prominent. There are some very nice detachable ones too, so you can pop it off when you want to read a book or watch a video. The paper-like screen protectors, besides being non-reflective (which might be a plus in rooms with overhead lighting), make everything less slippery and more similar to writing on paper, so there's less getting used to.
I don't go to school anymore but I'm taking notes on an iPad pro for work since when they came out basically, and I would say that also the software is a barrier in terms of how someone thinks and takes notes. For example the Apple Notes style of having an infinite scroll for a single note doesn't really work for me, as navigating it later becomes a pain. Software that mimics an actual notebook with single pages might suit someone who comes from paper better. Having the space limitation is actually a nice constraint (also because you have in infinite amount of pages).
The actual writing tools on the note taking software make a big difference too. Beside the pencil tool (still vastly superior to any other software I tried - and I tried them all), Apple Notes has nothing special to offer. A lot of the early, snazzy, note taking apps that came out when the Pencil arrived had fancy looking tools that proved to be terrible when doing actual work (I'm looking at you, Paper by 53). In this regard, less is probably more and when you have a good, fast (not lagging), dependable pen tool and a highlighter you're pretty much done.
All in all, as everything work related with iPads, the most important part is that you have to make an effort first, and commit to the change to do something you did elsewhere on the iPad. It might be difficult and it requires an open mind to learn and accept that things might get done in a different way from what you're used to. It will also take more time at first, but without these small sacrifices it will be hard to discover the upsides later on.