I use apple notes a lot. I love that you can add pdf or photo attachments and you can very rapidly type in when you are using the app in the iPhone.
For pdf annotation, nothing beats PDF expert, by far the best pdf app.
I also use notability for brain storming, it has an excellent integration of the pencil (draw with pencil, scroll with finger), while in other apps there is usually an extra step when you want to draw with the pen.
All three are excellent apps with different uses. I use them for different uses.
Another app to consider for pdf-note taking is Devon think to go. It has some different strengths and weaknesses. No iCloud sync though. Marginnote is also an interesting app for pdf annotation, but it is more complex than it should be.
My personal workflow is now leaning towards:
Adobe acrobat on my mac for initial pdf editing (such as adding links to pdf), reading the pdf on my iPadPro with PDF expert.
Typing in quick notes (to do lists) on the apple notes. Apple notes offers the fastest way to type in notes and to retrieve them.
Devonthink to go for local storing of sensitive documents (it manually syncs over wifi between iPhone/ipad/mac). Medicine is one of the business areas that has very strict document storing security regulations (almost all cloud options are NO-NO)
As I have written many times, I love my iPad, I wish I could do all of my work on an iPad. However I still do 40% of my work on my 12in retina MacBook. I love this machine for anything that involves typing. I also like using it when I am lying on the bed, because the keyboard acts like a stand.
Having said that, I am looking forward to the new iPad Mini. From testing it at the best buy store, I realized that it offers a very rapid thumb typing (optimal distance of the keys for my thumbs) and a very convenient one hand holding function (very light and compact).