I've come up with an idea of PDDF (Portable Data Document Format). The PDF format allows embedding files into documents. Why not embed an SQLite database file right in PDF document with all the information nicely structured? The both formats are very well documented and there are lots of tools on any platform to deal with them. Humans see the visual part of PDF, while machine processing works with the SQLite part.

Imagine that instead of parsing a PDF invoice, you just extract the SQLite file embedded in it, and it has a nice schema with invoice headers, details, customer details, etc.

Anything else in PDF would work nicely either - vector graphics, long texts, forms - all can be embedded as an SQLite file in a PDF.