I've mostly been using Remarks for the past few months. Not because its the most feature rich per se, but because I think the design is nice and it has pretty much of the features I've needed. Also, I have a few other apps by Readdle (its makers) and those have been good to me. Lately, however, it has become incredibly slow for me when writing in zoomed in mode. Up to the point that its really unusable. I am using an iPad 3/ a new iPad so that can't really be the problem. Nothing seems to help, I've even rebooted my iPad a couple of times which I usually never do.
Then I noticed yesterday that Noteshelf was discounted to $.99/.79 and decided to try it out. I'm very happy I did, because so far it has been great. It is a beautifully designed app that has a bunch more features than Remarks, which I haven't yet used very much but seem to be nice extras. Furthermore, on my iPad it just seems to work much more smoothly and it's so much less frustrating because of that.
I have also tried a bunch of other note taking apps; Note Taker HD, Notes Plus, uPad, Notability are the ones that come to mind. Out of thee I think Notes Plus and Notabilty are definitely best. The reason I don't use either of them as my main note taking app is that I just hate the way they look. Their UIs are intuitive but I think both apps simply look ugly. I may be nitpicking here but design is just something that is very important to make me feel comfortable using the app long term.
All in all, if Remarks would get an update to be a little less slow for me, I would maybe start using that again. As it is, however, Noteshelf offers a beautiful UI, smooth performance and all the features I need and I'm very happy with the purchase that I've made yesterday. Don't know if the sale is still going on but I highly recommend it.
Edit: checked and Noteshelf's sale is still going on right now.