The App Store app isn't particularly great, either. There are many UI paradigms it ends up breaking, and of course, it still goes for that sidebar/main window layout that all the Marzipan apps use.
There are a number of buttons that do follow iOS style though. Also, "Redeem" and "View information" open up views that were previously unavailable except through iTunes, and you can see a mishmash of styles there too.
The two things that infuriate me though are the font size of the sidebar, and the laughably placed "Done" button on the top right when you're viewing a story.
Having said that, I suspect the use cases of notes are quite varied, so a one-size-fits-all approach might not be straightforward.
You mean the actual sidebar (with the top level note folders) and the notes list? That has been the norm in 99% of note apps (and similar 'bucket' apps) for ages, across platforms...
So?