This isn't news... it's never news. Every single update to iOS seems to come with throngs of people saying it ruined their battery life. I don't know if it's app incompatiblity, the way iOS updates, or legitimate bugs on Apple's end but it happens every time. Even smaller updates like 4.1 to 4.2 have these complaints. The major iOS releases definitely all had complaints from new and old phones alike.
I'm not normally one for conspiracy theories, but it happens so regularly that it seems like it's almost in place to force the jailbreak community to wait for the "battery fix update" that's always right around the corner. The jailbreak teams hate wasting a crack when they know an update is incoming.
I think it's safe to say that it's Apple's fault legitimately.
Small updates like 4.1 to 4.2 to 4.3 introduced certain changes to UI behavior (visible in the configuration file if you jailbreak) and certain filesystem relocation so some things may not work as they did before.
The actual changes are probably a lot more sophisticated than just saying that they changed a file or two. Usually, that means older configuration files and older system file formats would not work. Which is why you can't restore a backup of a newer firmware into an older one. But that also means that the conversion of an older file format to a newer one would cause problems. Configuration files, contact database, SMS database, among other things, may experience issues, and that's perfectly expected.
Apple is sincerely not perfect. They have bugs in their firmwares. Developers get first dip and they complain the hell out of it, then when it goes public, the public gets to complain about it, and Apple takes the feedback, goes back to the drawing board, and start fixing stuffs. It has happened to every single beta since at least 4.0.
The iPhone 3G is a very good proof that Apple makes mistakes. They don't make as big mistakes as the 3G anymore (or at least not yet), but based on the number of bugs still residing on the bug report page, I wouldn't suspect that even iOS 6 still has some of those annoying ones.
At least they fixed the checkerboard pattern in Safari and WebView by replacing it with solid background color... That feature was requested so often that it seemed silly.