It is not just Amazon. Sony has terrible PDF support on their readers. I'm not sure if any e-Ink reader from any manufacturer has a good PDF rendering engine that works well. Even Acrobat Reader for computers is lackluster IMHO.

PDFs were never meant to be used on readers, they were meant to allow people to exchange copy protected documents designed for printing. For example, if a manufacturer of software wanted to electronically deliver a customer a tamper proof User Guide and did not want them to change it and redistribute the modified document. Or a lawyer wanted to distribute a legal document without worrying about it being modified. Unfortunately, PDFs got repurposed and were soon used in many other ways. Too bad as PDF is a terrible, memory glutten document format. They are not that flexible or usable even on a large computer monitor.