In main menu, add "custom" order for notebooks and folders. Add this where it says "name", "date", and "type" on the top of the main menu so you can keep the books in an order you prefer.

Make folders more customizable, add option to change colors of folders or add designs or icons to folders, similar to notebooks so that it is easier to distinguish folders and find them with ease.

Add a "folders" section to display only folders on the righthand side of the main menu page where it displays "documents" and "favorites". It would also be helpful to add each folder to this option to select each folder with ease.

Add a dropdown for folders so you can view its documents without having to enter a second page with the folders documents. This way you can see everything from the main menu and it makes it easier and quicker to find and stay organized if you could expand/minimize the folder.
This could be done in a cascading style when in the list form with a little arrow.
In the block form you could have a folder open with an arrow revealing a sub section block. I believe this is called something like a collapsable mega menu for mobile devices.
You could also do a preview of the folder when you scroll over a folder, which would work on devices with a mouse, or you could use the "hard tap" function with pressure sensing devices.

Add merge/combine/insert/move entire notebooks or documents from the main menu so you don't have to move them page by page.

Add a hyperlink option so you can insert and view a document page in another document. If you click on it you could also add a href to go directly to that notebook/document from where you are. This would be super useful when organizing a lot of information.

Make a ability to hyperlink sections directly to a page. This would come in handy when you have the calendar or notes and you could add like a sticky note icon or something that would direct you to the page it referenced on another page/tab. For example if you have "assignment" due on specific date and add a hyperlink icon it would take you to "assignment" you have referenced on another page.

When making idea boards of you could have the images, sections, or words have an ability to hyperlink so you can go directly to page from app.

When importing/pasting text add a "clear formatting" option to get rid of background color so it inserts nicely, currently you cannot even get rid of background text color.

Make it possible to editable text like a .docx or .doc, not just .pdf.

When importing a editable text, make it so you can edit the document itself without having to typeover it as though it is the background of the page. import the text itself.

Add a document section to make "word" type documents so it can be used for work and school to submit work without having to use multiple apps.

Make ability to import styles or presets from other people.

Make "shared" documents/notebooks/folders so you can collaborate with other people with the app.