Better organisation options through internal links!! When you have a lot of notes you don't want to be searching through hundreds of pages for the specific topic your looking for! I would love to be able to create an index where I click on the topic and it will take me there, like google docs does (one of my favourite features). Maybe different personalisation options side tabs like a binder and you can click them to go to the specified area (as a seperate option not instead of basic internal links). I have found people asking for this as far as 3 years back and people changing to different note take apps for this reason and its so surprising that it hasn't been added yet. Also don't do it so you can only choose a page, but you can choose key words to get the exact point!
Yes, a hundred times yes!
Internal linking, both within a notebook and to other notebooks, would elevate GoodNotes into a whole different tier.
Henna DP commented
this is extremely critical for your organization, as this feature has been available to your competitors (ie Notability) for some time now. i am even considering switching on over to their platforms if this continues to effect efficiency.
I am not sure if i understood you, but i would add to your idea a feature where you could link other documents from goodnotes. It could work like linking a website in a word and by clicking the link the other document would open. This would extremly simplify organizing learning material especially in math.