There is exactly one iOS app that decently reads both ePub and PDF books. Apple's iBooks. And they destroyed it this fall. First they excited everyone in the Mac world with the new OS X Mavericks that includes a desktop iBooks app, only to reveal upon release that you can't add or change any metadata in your library at all. Ever.
I have a LOT of ePub books, both purchased from iBooks and sideloaded form elsewhere. And I have a CRAPTON of PDF books. I don't want to read and organize them in different applications any more than I want to have paperbacks on one florr of my house and hardback on another. That's stupid.
Oh there's reader apps out there. Kindle (kindle format only. So, useless). Marvin (looks great but only epub. Their next file format priority is FB2... are you kidding me?). Goodreader (brilliant, but PDF only). Bluefire (ePub and PDF, but remember, the app has to be decent).
That leaves iBooks. Which is fantastic at exactly one thing (reading) and shit for everything else (organizing, interface with desktop, notes).
Look. If I wanted a shitty experience that I wanted to have to noodle with every goddamn week, I'd use Windows and Android and Google Play. I sure as hell didn't stay with the Mac all this time to have my music player turn to crap, only to be followed by my eReader. What the actual fuck, Apple? iTunes has sucked for months and i learned to accept its sucking because it's still marginally usable. But now you fucked with my books and I'm mad. I'm glad Jony Ive is on the software team now, but if he's behind all this crap, he should have his knighthood stripped.