I think you're grasping when you claim that PDF is a "very problematic format":
* full text search works fine; much better than on your site. Try searching "hospital" in both and see which gets better results (spoiler: its the PDF)
* Yes, a comprehensive report is impossible to scan-read. That is kind of the point of a comprehensive resource, don't you think? At best, scan reading your site (an opaque javascript visualization) leads to an incomplete understanding; scan reading is rubbish for understanding.
* If you want to do Excel-style data analysis, neither your site nor the PDf is the best choice; you should be looking at original sources, just like the USA Facts team did.
Giving people a pile of facts from which to cherry-pick for arguments isn't helpful. Promoting a deeper understanding of the government and its workings does. USA Fact's visualizations, tied back to the Constitution (perhaps the most underappreciated document of our time), promotes deep understanding.
USA Facts ultimately does a much better job serving two audiences: 1) the people who need a better understanding of the big picture of government (on the main site) 2) the people who want to dig in and understand the nitty-gritty - the PDF.
You have a good product, and I normally wouldn't be so harsh in my criticism, but the arrogance in your statements demands correction.