The comparison is easy:
- Creating PDF entirely from scratch on every page view: use FOP.
- Merging existing PDFs and/or changing existing PDF files: use iText or similar tools like PDFPrepTool.
It's easy to take XML data and put it on a PDF using iText, it's also easy to convert non-XML data to XML to use FOP. It's more a matter of how much you want to code versus the strengths of the tool.