You can now use GoodReader to annotate PDF documents which includes adding sticky notes, text highlighting, freehand drawing and more through simple gestures. The annotations are stored permanently in the PDF file so you can see them on your desktop based PDF readers as well.
Related: How to Edit PDF Files
To add an annotation in a PDF document, just do a single tap in the region and hold your finger until the annotation toolbar appears (see the above screenshot). If you would like to edit an existing annotation, hold your finger over the annotation for a while and you’ll see an option to edit or delete it. It’s all quite intuitive.