I’ve not ruled it out. I prefer cloudkit which seems more reliable. I’ve just seen too many forum complaints to do with icloud. I’ve found syncing my own files is ok in general, but there are times when it just doesn’t sync what I need when I need it. I use it, but not for critical files or time sensitive files.
NotePlan uses cloudkit to sync if that’s of any interest to you.
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Well, then you’re in luck:
Drafts syncs using CloudKit, the same iCloud technology that lies beneath iCloud Drive, Notes, and other Apple services. It does not sync via files.
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And it has worked really well for me.
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I agree. The sync works really well.
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As described and elaborated on as the thread progressed, your requirements are sophisticated. Use a Macbook and the more sophisticated apps available there as your base. if you must use an ipad while being portable, then just use it and integrate that stuff manually if necessary. avoid looking for nirvana unless you are willing to accept lowest common denominator. without mind reading i suspect you will not want that.
keep it simple. use a macbook as main computer resource. focus on your learning and not the IT
i have been there done that.
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That might be just the wrong approach.
Instead of looking for a note taking app, that might be convenient for you, you should define what you really need, and then look for an App, that fits those real needs!
Millions of people all over the world are using the iPhone/iPad for their Notes, so why should you not be able to do so?!
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Were it me, I would take notes by hand, then keyboard them later on a Mac. It’s a sure way of concentrating on what is being said, remembering it and then reviewing it when you keyboard the notes.
The iPad COULD do what you want, but it would be needlessly labor intensive, and involve lots of kludges and a keyboard. If you want or need to take notes with a device, use a MacBook, For me, I found the technology was distracting when taking notes during class/lecture. I do like using the iPad to take notes while I’m reading, especially ePUBs and PDFs.
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Fair point. I was thinking of the “make it work” users. It would perhaps hit iPad Pro sales harder then. Although there is that cadre of users who buy a 12.9" iPad Pro, or a Mac Pro just to do email. 
Entirely possible, the M1 iPad Air might do that. I have no plans to replace my 2020 iPP. It would be nice if Apple allowed it to run full screen on an external monitor. But I only use one occasionally when I’m editing video at home.
Why has no one mentioned Devonthink? Based on the requirements it sounds like it meets them all. Although I don’t think you’re looking for a note taking app as mentioned, given the requirements beyond just taking notes.
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OP did, near the top:
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I wish that I could like this comment more than once!
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Ah…. Missed that! 20 characters…
I would suggest you investigate Alfons Schmid’s Notebooks.app. The latest version does backlinks as well as wiki links. You can drop and search in pdfs, but they will open in your pdf app of choice. Multiple sync options. I use iCloud and haven’t had any problems.
That said, if I was to write a major project like a thesis I would want to do it on a Mac. I’d use the iPad for notes, but the Mac would do the heavy listing.
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I’ve been toying with the idea of using Notability which I own. It also has the ability to record the class audio. The extra write up of the class notes would help solidify the lesson.
University policy may allow instructors to prohibit video and audio recording of lectures. The proviso especially now is that recorded lectures are available from university-sanctioned methods, e.g. Zoom or Panopto.
—
JJW
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What benefit would that bring?
Lecture content can be subject to copyright guidelines if not also to the thereby afforded entitlements.
The “benefits” are to protect against infringement of such potential entitlements as held by the university if not also the instructor.
—
JJW
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I use Obsidian for this plus GoodNotes on the iPad.
I use the iPad as a note taker or like a piece of paper. The resulting notes, just like when I was doing it all on paper, still go to me Mac machine and get cleaned up, or deleted or otherwise processed fully.
I would never think to actuall try to write long texts, create presentations or data analysis on my iPad.
Now Obsidian on iPad has its issues. I tend touse it more as a reference and do most of my writing/note taking in Goodnotes, use text recog to get them into markdownand into Obsidian and hten final clean-up on the Mac. Bonus is the multistep process means I am reviewing the material at each step and that improves the overall content.
For scientific papers I use Zotero, and do annotations on iPad and then into Obsidian. For Books I am exploring several options but all focus on using the iPad as a reader/annotator/quick notes and then final work in MacOS.
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