GoodNotes and LiquidText for lectures and papers respectively. There is a significant amount of path dependence in those choices.

Youtube reviews are probably the best way to get a feel for the current competitive landscape (e.g. GoodNotes vs Notability, MarginNote vs LiquidText).

Our paths and final choices sound similar.

GoodNotes made a lot of right choices, and LiquidText is especially under-appreciated:

https://www.liquidtext.net/liquidtextadeeperdive

I've been using a 2 in 1 Linux laptop for similar use cases, but the software options aren't amazing.

How well does the iPad handle hand recognition when using a pen? Does it accidentally scroll down PDFs or lag when you are switching from pen to fingers to zoom or pan?

The apple pen, touch recognition, palm rejection, and 120Hz + low latency are truly spectacular. I don't want to say flawless, but that's purely on principle, I can't think of a single screwup. Even my (employer's) macbook pro has a palm rejection failure about once a week, which is very good, but the ipad is better still. The base OS and websites have silky smooth scrolling, ditto for PDFs, even gnarly text book PDFs with scribbles everywhere. The pencil is super accurate, it has no problems hitting 1x1mm (or 2x2mm maybe) badges in LiquidText, and the size is perfect. It looks too big, but it's smaller than it looks. Apple did a good job earning their Apple Tax on this one.

You can get an iPad for $329 and a Pencil for another $100. There isn't much of an Apple tax in that at all. If you factor in the price of software - Procreate for $10 and GoodNotes for $8 - it's a pretty amazing value.

Since you mentioned a 120 Hz display, I assume you’re talking about using the second generation Apple Pencil on an iPad Pro? A sibling comment pointed out the much cheaper price of the regular iPad (which only supports the first generation Apple Pencil) so I thought I should chime in to say that my experience with the first generation Pencil does not reflect yours. Writing is laggy and imprecise (I can write legibly at about half the size on paper), charging with a Lightning connector is extremely awkward, and it needs to be done almost daily because the battery drains continuously [1]. I‘m still a big fan of the iPad, but I gave up on the Pencil after two months and switched back to paper.

[1] https://discussions.apple.com/thread/8231431

Apple Pencil 2 is definitely a big improvement on the first one, primarily because of the charging mechanism - the first one was always either out of battery or I couldn’t find it when I needed it, as charging it felt stupidly awkward and there’s no way to attach it to the iPad. The second one just attaches and charged magnetically so it’s always there and charged when I need it, making me much more likely to use it (and I do, all the time).

It does feel quicker and more accurate too though I wouldn’t say that’s a dealbreaker for the first gen (I also upgraded to a 12.9” iPad which I think makes a bigger difference for note taking etc, maybe because you end up writing a bit bigger than on paper so the extra space is useful?)

Yeah, I've heard that 1st gen Apple Pencil wasn't very good. I can't speak to that myself. I have an iPad Pro 2018 and an Apple Pencil gen2, it's my first iPad, and I love it.

That's good to hear, I might have to swing it for an iPad and pencil.