OneNote is the only great note taking software for the Surface. In comparison to Goodnotes, it is FAR more powerful which is both good and bad. I've been using OneNote for many years, and need Windows for work, so it's easy to integrate into my workflow. Still, I really like the dedicated simplicity of Goodnotes.
This is my second Surface Pro, and the first time it is really sticking for me. I am a huge, huge iPad fan. I'm on my 4th with the Air 2, upgrading nearly every year after skipping the 2 and 3. You are right; there are certain things that the iPad does far better than the Surface, and others that just take being willing to do them a different way. The battery life is no contest. Yet, in spite of myself, right now, the SP3 is sticking in my workflow far more than I expected. The stylus works how a stylus should. I actually like the bigger screen a LOT more than expected for reading - my Air 2 feels tiny in comparison now. The 3:2 form factor is also awesome - I actually feel like I have a big enough canvas to do real work when I have the keyboard attached, yet have a real paper replacement when I use it as a tablet in portrait.
I have a lot of apps that I can't find direct replacements for on the SP, but for most I am finding work arounds. It has been 6 weeks or so, so not a ton of time, so it's possible I'm still in the honeymoon period. I'm doubting that more and more every day though.