Recently bought an iPad Pro 12.9" and Apple Pencil for taking notes at university. Most of my note taking is maths related so typing notes isn't the best option for me. The iPad is pretty much the only experience I've had with digital note taking apart from a brief stint with a relative's SP3.
If we're talking purely about the feel when writing I found that I preferred the iPad to the SP3 by a large margin, mainly due to latency. My handwriting is still a little messier on the iPad than on paper due to the reduced friction from writing on glass but its not a huge difference. I can't comment on how the writing experience is compared to newer surface products as I haven't spent much time with them. In terms of comfort I haven't had any issues with the Apple Pencil, I regularly spend 4+ hours writing with it at a time and it's no less comfortable than a normal pen for me.
The lack of additional buttons on the Apple Pencil is annoying at first but you get used to it, I would still prefer a design like the surface pens though. Battery life also isn't that great on the Apple Pencils, I find that I need to charge it on almost a daily basis if I'm using it heavily. It does charge quickly though and you can always top it up by plugging it into the iPad itself. Another issue with the battery is standby drain, if you leave the pencil connected to the iPad it will remain active while it senses movement causing the battery to drain pretty quickly if you're storing it in a backpack or moving around with it. The solution to this is to disconnect the pencil by disabling bluetooth however this requires you to plug the pencil into the iPad every time you want to reconnect it.
As long as you have a laptop or desktop the iPad is fine, I definitely wouldn't recommend trying to replace a computer with it due to the limitations imposed by IOS but it sounds like you understand that.