I've been using iAnnotate for quite a while on the iPad and generally like it a lot. This is my main use of the iPad, taking notes on journal articles and grading students' papers.
But, one downside of iAnnotate is that it appears that they have not kept up to date with their iPhone version of the program. The iPhone version, which I haven't used in ages, lacks some of the newer features of the iPad version, most importantly syncing with Dropbox.
I came across this forum and based on the info decided to try downloading PDF Expert to my iPhone. I figured it would give me the iPhone functionality I needed and meanwhile let me test out the program in case it was worth getting for my iPad as well. I don't expect to do a ton of annotating on my little iPhone, but it's nice to have that option because it means I can get some work done no matter where I am.
I've only played around with PDF Expert for a few minutes, but I've already identified two issues that are deal-breakers. First, the process of creating an annotation in PDF Expert is way too clunky: tap and hold until the menu comes up, but the hold only selects a small portion of text so grab onto one of the tiny (especially on an iphone) handles to expand the selection, then tap on the menu to choose the type of annotation you want. And if you want a different color tap on the annotation again, choose colors, and choose the new color. Way too many steps to do over and over again. I like iAnnotate's approach of selecting a tool and creating as many annotations as you want with that tool until you turn off that tool.
The second issue is that there are no options for freehand tools (e.g. pencil tool). I use the pencil tool quite a bit (stars next to important points, arrows, etc). Also, some of the articles I read are old-school pdfs or scans of books where there is no OCR'd text to highlight. In those cases freehand tools (pencil tool or even better iAnnotate's new freehand highlighter) are the only options. iAnnotate also has a lot more options for different types of tools, colors, and customizing the toolbar.
So, although I appreciate having a program on my iPhone that syncs easily with Dropbox I'm going to stick with iAnnotate on my iPad. iAnnotate is not perfect but it's improving with each update and seems to be way ahead in terms of annotations. It's possible other apps are better on other fronts, perhaps forms which I rarely use.