What orientation do you read in?
I have made a strange observation after extensive reading on iPhone and iPad. I am most comfortable reading, a novel for instance, on the iPhone, in portrait orientation, using the night theme, and turning pages instead of scrolling. On the iPad, I like to read, a PDF document for instance, in landscape mode, using the day theme (i.e. white background), and using scrolling instead of page turning.
I have yet to figure out why that is so. It could be because PDF documents need to be wide for the text to be big enough to read, and the iPad resembles the PC form factor where reading has always been done on a wider screen. There is the kind of reading, a magazine for instance, when I usually read with the iPad in portrait mode.