I want to like the Notes app but I can’t seem to change the size of pencil tips like OneNote or Notibility and various others.
And @twerpoet. I find I use the Notes app for just quick reference things--digital library number, quick lists that I want to keep or add to, etc. I use Noteability for everything else--PDFs with annotations--or to create my own PDFs, scanned info, all kinds of notes and tutes, etc. It immediately updates backup with Dropbox if you connect with it. I like the fact that I can type info, add handwritten notes maybe add photos or scanned info or even print screens. I use both often (Noteability actually daily)
I was a long long time MS Office user but have found that Pages, Numbers work fine, I use both for our business purposes--and use MS Office (I have the 12.9) to check formatting. I generally send Word docs in PDF and they will maintain correct formatting. I did use WPS Office too--works pretty well, but if you are going to do a great number of docs or spreadsheets, probably better to go the subscription route for MS Office.
I used to use GoodReader all the time but generally use Ibooks, Kindle and Noteability and deleted GoodReader. I would recommend Documents And/or Icloud Drive but the new File app in IOS 11 may work fine. I have used Dropbox for a long time, not only for backup but to have the ability to access files from all my devices (Macbook, Iphone and Ipad).
I would definitely recommend the Pencil--use it every day. I recently bought the Logitech Combo keyboard case and like it a lot--and the fact I can quickly detach and attach the keyboard is one of the reasons plus the very good kickstand for about any angle--it also is backlit. I would probably recommend a good keyboard--I have a Logitech with a good angle to it for nice typing but there are many--bought it very reasonably when there was a good discount through 9-5 Toys.
There are quite a number of apps that I use often but each is fairly specific to things I do--you will find what you need and can ask for specific app recommendations when you get your Ipad. Unless you are a photographer you will find Snapseed in conjunction with the Photo app to fill your needs--I'm now using Affinity Photo but unless you need a Photoshop style app I wouldn't recommend it-quite complex. I use Readdle's Calendar 5 and would recommend you consider a PDF converter if you find the need to convert things to PDF but understand there is a converter in IOS 11 as well as being able to scan with the Notes app--I use Readdle versiosn of both of these.
Just as a note--I was a Windows user since Win3.1. I gradually moved to all Apple since Ipad 1. I have a 15" Macbook and upgraded to the Ipad Pro 12.9 about 18 mos ago. Over the years with Ipad I learned with workarounds I could do a great deal with them and with each IOS upgrade it got better-and at times I would use the Ipad as a second monitor when I needed that. I really look forward to IOS 11--my only issue which I don't expect to change--maybe ever--is I can't access my external drives (I have photo files from 1999 forward on them). I do carry a portable BT drive when I travel that does work fairly well with its app and I can transfer to my externals via my Macbook. If you need to transfer files between Win and Apple devices, consider Dropbox or similar-I use it to backup all our business data and my own data as well.