I agree with some of those complaints, but I am getting very sick and tired of people complaining that Apple let them down because they didn't slap a new coat of paint on the OS just for the sake of slapping a new coat of paint on it. It's a curious thing to note in the article that Vista made changes to XP, when Microsoft has just revealed that all of those visual changes (i.e. Aero) are getting scrapped even in the traditional non-Metro experience in Windows 8. Making changes without clear purpose is foolish.
The core idea of iOS is that the OS is just a shell. Want something new? That's what apps are for. You can do anything you want in an app. All the OS is there for is navigating the apps. What Apple needs to focus on is providing the hardware to allow app developers to continue to do new and innovative things--and where they've most notably failed to do that right now is in offering a Siri API. But presumably the new iPhone will have NFC and that will help push the envelope forward in that space.
As far as the OS goes, I would like to see some of the UI inconsistency corrected (and streamlined between iPad and iPhone--I don't understand why there is any difference in experience when you use one versus the other), and there are some obvious usability features that Jailbreakers corrected a long time ago, that for reasons passing understanding Apple has not. But aside from that, my biggest concern is that Apple is spending the majority of its time the last couple years undermining Google (Siri to replace search, Maps to replace Google Maps) rather than pushing the iPhone forward.