Umm, Goodreader?
No mention of Goodreader? That app is great on so many levels: can invert colors or even read with a red text/brick red background, which is really easy on the eyes. Not to mention the fact that loading up books in it is stupid simple thanks to its integration with Dropbox.
Sure, iBooks looks pretty, but it's like every other piece of Apple software: it lacks customizability and assumes one shoe fits all feet.
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