Thanks for your comment! By complicated PDFs, what do you mean exactly? A lot of pages? With forms? I've tried with standard technical books I have bought.

The pdf-diff tool simply captures a sort of "screenshot" of a PDF page and then compares it against to the page from the second PDF file you'd like to compare. Since it works by comparing raw pixels, I guess it'll work with complicated PDFs.

Now "working" does not mean it's a good result for the eye and this is why I asked for help regarding some issues.