The problem with PDFs on the iPad is that few, if any, actually do the rendering themselves. Instead they are just using the basic CoreGraphics rendering of PDFs, which has some known limitations. On the Mac you have access to PDFKit, which can render more PDF features, but Apple has yet to port it to iPhoneOS. A good test of whether or not your iPad app renders things themselves is whether or not they support graphically selecting and copying text.
I find the PDF support for iPad kind of annoying. GoodReader is okay, but it has a travesty of a user interface. There are lots of others out there, but their descriptions lead me to believe they use the same basic rendering techniques and I’m not really in the mood to keep throwing money at the problem until I find one that does a better job. It would nice if the app store had a try before you buy feature.
It’s possible to write your own renderer on top of the CoreGraphics foundation. I’ve tempted to just bite the bullet and do it myself. I have a lot of gaming PDFs and I intend to make fill use of the iPad at the table.