Tis has been my #1 complaint about the iOS system.
When I got a newer iPad and updated my reading apps to be compatible with (at the time) iOS 5, iTunes overwrote all the apps, so the next time I synced my iPhone 3G, it copied the newer, incompatible versions. Which then failed to open on my older phone. I haven't been able to read on my phone in quite some time.
That really penalizes Apple's most loyal customers, who own multiple devices. I'd love to update every time Cupertino announces something new, but I suspect that's the exception, not the rule.
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