Further, the minimum brightness on iPads is still blinding. You have to download a specific "night browsing" browser just to get it to go lower, and if you are in an ebook reader, you are reliant on them having something to help.
Ultimately, I found that for ebooks I'm just way better off with one of the new Kindle Paperwhites, which I'm absolutely in love with. However I still find myself wishing that they had a native way to invert the colors of text. This is trivial to do with common ebook/text doc formats, and I really wish they'd make it an easy "night reading" feature. Having the entire screen with a white background causes unnecessary eye strain and brightness when reading at night. Reading white text on a black background is SOOO much easier on the eyes in a low-light situation.
Taking it a step further, while I hate backlit screens for night reading, one of my favorite reading setups is using a "terminal green" on black in Stanza on my iPad. Now if only the Kindle Paperwhite could do color...
You should consider getting glasses or altering your prescription. And if you're suffering eye fatigue it's probably not a great idea to be reading on a screen late at night regardless of the colors. Research "eye strain" for other suggestions that may help you.