[belden]

This is just my opinion so others may feel completely differently but of the three, epub is definitely the one to go with. I say this because there are a bunch of different readers that will let you read epub files and I like customization which really only epub will give you a lot of choice with.

PDF is great, especially on the new iPad's retina screen, for replicating the exact layout of a printed book. The problem I have with PDF is that that's really all you can do with it. Again, others may have some app I've never heard of that will let you change the font size or typeface of a PDF, but in my experience all you can really do is flip from one page to another and read it. And you mentioned using Calibre, if you ever want to convert PDF to another format it is possible, but in my experience it never comes out as well as I'd like and a lot of times you'll get things like the book title or page numbers between paragraphs which I find very distracting.

Mobi is good if you want to use the Kindle app and really, that's the only positive thing I can say about it. I have nothing against Amazon, I have a Kindle and I've purchased a few books from them, but I don't like the Kindle app on the iPad. You only get one font, there are only six size choices, and you have no control over the margins or line spacing. Like I said, I like customization and setting up the text just how I like it and the Kindle app is way too limiting to me. Plus, side loading has always been wonky for me, covers don't show up, things like that. And if you have epub files and you do want to use mobi files and the Kindle app, you can easily convert them and they come out pretty much perfectly.

The thing I like about epub is that besides being supported by basically everyone but Amazon is that like I said, there are a ton of readers that you can choose from. I personally use iBooks because I like the way it displays the text, the things like the pages left per chapter in the bottom corner and the general presentation of the app. I'm sure others disagree but I've tried nearly every app I could find and it's the one I always come back to.

Finally, let me just say the great thing about the iPad is that you really don't have to choose. Almost every reader app is free so you can try them all and find the one that you like the most.

EDIT: After writing this, I saw that Bluefire Reader had JUST been updated for the retina display. I have to say that from what I've seen so far, it does look like it may be my new favorite reader for epub files.