Are you using any particular app for viewing PDF files on the mini?
Very good question. I had bought from the days when I owned a gen 1 iPad the app Good Reader. While it is excellent, I want to synchronise my PDF viewing (and annotating, which is a big requirement for me, given the school nature of my PDF reading) so I went ahead and splurged on PDFpen for iPad, as I have PDFpenPro on my iMac. I've also tested the iBooks application, as it displays (and features specifically) PDF files.
Good Reader is great, it's what I first viewed PDFs on in the app (other than the default viewing of Dropbox).
PDFpen at first I was annoyed because it retains a small part of the title bar (the iOS title bar), which Good Reader doesn't, but also because it doesn't fit the entire page by default, I had to keep shrinking it to get the whole page in the display. What I now think is that PDFpen not shrinking each page is a good thing - I read a lot of scanned PDFs, and having that bit of extra zoom (even if you have to scroll down the page a little before moving to the next page) is worth it.
Using iBooks (a quick test admittedly) is a very basic PDF reader, and certainly able to display a PDF. I was even able to read a full PDF page in landscape mode (when the PDF is in portrait), which is more an indication of the mini's screen resolution being good enough to display portrait PDF pages clearly enough in landscape.
I also tried (quickly) these same files in the Kindle app (which I also have on my device) and it rendered them nearly the same, though I noticed when it displayed pages it would pause rendering them until it could render them perfectly, where iBooks might render them quickly with blur, and then render them perfectly. In the end, they both render the same, but it appeared to me to be a different way of handling the files.
One feature I thought might be interesting, and maybe one or all of these apps do this, but it'd be good to be viewing a PDF and have an option be "eliminate white space around the page" (which is similar to what the desktop version of Adobe Acrobat Pro can do, not easily mind you) - so it would automatically zoom in to a point where there is *only* text (or images) for each page, and that would effectively maximise the text area of the page in the display (automatically). That would be cool, I would like that.
All in all, I'd say all those apps are quite similar at viewing PDFs. I'm just well pleased with how the device displays PDFs in general. Hope that helps.
