Don't miss out on GoodReader, although it's a paid app, but not too expensive. It's been the general consensus that GoodReader is likely the no. 1 app for PDFs in iOS.
I agree that converting PDFs to EPUB often produces horrible results and isn't worth it. I only advocate converting between MOBI and EPUB, because those two formats are somewhat related.
As to fan fiction writers, it's their mistake to be publishing their creations in the PDF format at all. At any rate, they shouldn't be publishing them exclusively in PDFs -- these are no longer the 1990s or even 2000s. PDFs are best suited for printing, not reading, and definitely not reading on small-screen mobile devices.
Last edited by Faterson; 12-13-2012 at 10:12 AM.