ePub has worked as good on the iPad for me as it does on the two readers I have on Android. One thing to note is I don't see a way for the Kindle application to read files from iTunes or anything but download it from my library on Amazon. On my real Kindle I can copy my own files over directly. The iBooks application allows ePub so I have imported my non-kindle books there.
Another thing to note is a hardware kindle can't do what you want also in managing large amounts of books. Sorting by author, title, or recent does not help when you are trying to sort by collections or other things. So far the iPad with iBooks and the Kindle application is as good as my Kindle and its nice to see things in color with fast page turns. Its heavier but the extra things it does like movies, comics, games, applications, make it much better for me. I am giving my kindle to the wife
