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Not sure if this is what you are after, but I do have a 12.9" iPad and a Pencil...
Personally I use GoodNotes, as it syncs between my iPhone and Mac... It's really good, and I love the different colours, and the ease of operation... It's very natural to use, as you can effectively lay all across the screen and it won't respond. Best of all, you can back it up to DropBox/Evernote/OneNote (I think?) and most other programs.
I use Notability with an Apple Pencil on the smaller iPad Pro.
For general note taking it works well, my only grievances are:
* When adding drawings / annotations next to typed notes the drawings don’t flow with the text. If I add more text at the top of the note then the text flows down but the drawings stay in the same spot, so they’re not next to the relevant text any more.
* The erase tool erases the whole of the line you drew, even if you’re just trying to erase part of the line. Annoying if you drew something complex but just overran at the end and just wanted to tidy up the loose tail.
* This isn’t necessarily a Notability-specific issue, but I often use split-screen to work on a document and use Notability to make notes in the small section of the screen. When I go to review the notes later they’re scaled up to the full width of an A4 sheet making them far less useful.
Those gripes aside, I haven’t found a better note taking combination for the iPad yet.