I was wondering if there is a pdf reader-writer-publisher-editor that can add text, highlight, shapes and general edit an existing pdf document.
Something like Nitro in windows.
There are several FOSS options out there, none of which come close to the functionality of editors such as Foxit PDF Reader under Windows or commercial solutions under Linux. That's why I prefer to run Foxit via PlayOnLinux.
As far as native applications are concerned, Master PDF Editor is probably the most advanced free (as in beer) PDF editing suite available in Ubuntu right now. It's available from the Ubuntu Software Center but requires you to register an account with Ubuntu before installing.
A few months ago I stumbled on Quoppa PDF Studio, a commercial PDF editing solution that runs natively on Linux via Java. It comes with a very impressive featureset and is very close to Adobe Acrobat in terms of PDF editing functions. However, I have found PDF Studio to be a bit less stable than Adobe's solution when editing very large PDF files (≥ 500 pages).
Other than that I would say that PDF Studio is a very good, albeit expensive, piece of software and probably the best PDF editing suite out there on Linux right now.
You can download a free trial version here. It doesn't come with a time restriction. Instead, edited PDFs are automatically watermarked by the software to indicate that you're using the trial edition.
LibreOffice 4.0 opens PDF files in LibreOffice Draw where you can make all kinds of edits. I just used it to enlarge 80 images and move them around; it worked great!
If you are using Ubuntu 12.04, 12.10, or 13.04 then you probably have version 3.5, which does not have this feature. As I did, you can now force Ubuntu to upgrade to version 4.0 by typing the following in a terminal (press enter after each line).
If you don't have LibreOffice installed for whatever reason, then instead of the last line, type this.
Master PDF Editor (current version 3.3.20) for linux is pretty good and is available for Ubuntu for free. It has been very good for me, by and large and worth a try.
Recently I have been collating text books for my daughter and have finished more than 15 Higher Secondary textbooks from individual chapters available from National Council of Educational Research & Training, India, using Master PDF Editor (64bit) on Ubuntu 15.04. The average number of pages are about 350 with lots of illustrations, graphics, multiple columns etc. I could insert cover images, add book marks, remove water marks (individually, from each page, though), correct some errors. I could not get the default paper size of the document and had to extract the first page and reinsert delete content for adding exact size blank pages. It worked fine. Else, trial and error is the only option. You can easily delete unwanted characters, boxes, etc. But inserting symbols and subscript/ superscript is a problem. I copied and pasted symbols available elsewhere in the document. If you have to add content, probably you need to use another editor, I guess, carefully, matching the font, size, style, symbols etc. You may be able to get the details from document properties or publisher documentation.
I could do well in all, till I encountered with Class 12 Biology book, which contained heavy graphics, colors, non embedded fonts and other non-standard pdf stuff, perhaps. Master PDF Editor, started misbehaving, hanging etc. even for opening editable files, page navigation, saving etc. The files after simple removal of water mark, merging etc. got bloated nearly twice the size of the original components. Not able to process even a couple of hundred pages and cumulative file sizes of about 175 MB.
I have submitted this sample to their technical support and got a feedback that large files could be a problem and being worked upon.
Bottom line: Very good for standard pdf documents for editing. Pdf input and pdf/ image output. Check for non-embedded quantities in input.