It slipped my attention at the time, but Moon+ Reader added a number of useful PDF features a few weeks back. The paid version of this app ($2.49 in Google Play) now enables readers to annnotate the PDFs they read on their Android smartphone or tablet.
According to the change log, the app now supports "free text, ink, line, arrow, rectangle, ellipse, highlight, note", but that's not quite what I found when I tried the app. I've been testing my copy of the paid app and I have noted that the new options include highlighting, underlining, and striking through the text; I have also attached a text note.
I'm not sure whether my HTC smartphone lacks certain features or whether I just haven't found them yet, but I can say that the abilities I have found are quite useful. And here's where things get fun: the color used for the highlight/underline/strikethrough can be changed to any of 1.67 million shades, or about 1.67 million more shades than the highlight options offered by the big-name reading apps.
The changelog also mentions that the PDF thumbnail function, which lets you see the pages of a PDF as thumbnail sized images, is now faster and smoother. There's also a new tilt-turn page turn option for those whose thumbs are busy (it happens). Other updates include improvements to the book import procedure and a tweaking of the highlight renderer for Epub and other reflowable ebook formats. I haven't used Moon+Reader's annotation options enough to see the difference, but I'm sure it's there.
This app last crossed my desk back in August when I reported on a previous update which added support for Epub3 video. At the time I noted that it appeared to support right to left languages, but I lack the language skills to confirm this.
Update: The RtL support is incomplete. I've been told by a commenter that the page turn rendering doesn't go in the correct direction.