I second Noteshelf. I just downloaded it a couple hours ago and I'm pretty much certain this is going to be my permanent note-taking app on my iPad.
I've used Penultimate, Notes Plus, Noteability prior to this.
Penultimate had great inking but a limited feature set.
Notes Plus is like a bad Windows app. It gets a lot of love because it crams in every feature you can think of, but all of that is at the expense of a piss-poor design, unintuitive controls, and an ugly, UGLY interface. I had this app for the longest time and the recent update made it even uglier imo. Even the new logo for this app is ugly.
Noteability is a pretty solid note-taking app that I'd recommend if you want something similar to Notes Plus on a features level but that does it all better. It's a pretty decent, streamlined version of that and it works well.
Noteshelf, on playing around with it for the past few hours, immediately stood out to me as by far the best of the lot. It combines some very good inking (not on par with Penultimate but better than Notes Plus and Noteability) with a fantastic interface and controls. All the essential functionality I want is in this app though I should note that voice recognition and PDF annotations are not included (if those are essential for you, go with Noteability). But everything is just better thought out than the previous apps. It feels like an app that Apple could have put out - clean, elegant, and functional design.
The whole thing is very intuitive to use and I actually really enjoyed using this app, unlike the previous ones. My only wish is for higher-resolution PDF export (the handwriting exports at the resolution of the iPad, though the text exports beautifully). If they add that, this will be my perfect note-taking app.