i have an automator script to set up new epub from my calibre library (which i use to manage all my ebooks) right into itunes. then when i sync my ipad they show up. pdf files are stored on my webdav server and goodreader will pull those down from the internet where ever i may be. i don't even notice the margins in ibooks and don't really care. if i was reading a paper book i'd have absolutely no control over margins, brightness, fonts, etc. the fact that i have any in ibooks is simply a luxury. as i said, i like to spend more time reading than tweaking, crashing or being frustrated. since i travel extensively i want to be able to fire my ipad up on a plane and get to reading a book, not throwing my ipad off a plane because an app crashes.
generally my ipad has been rock solid, the times it crashes have been using iphone specific apps, and jailbroken applications or hacks. there has been only one ipad specific app that i have had any difficult with and can get it to crash quiet easily, repeatedly. i jettison any unstable apps and look for a replacement.
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