The greatest omission is that of a proper input system (read: SwiftKey Flow / Swype / T9 / SlideIt)! iOS keyboard doesn't come anywhere near any of these.
There are less significant ones, too (such as a lack of 3G switch in the Control Panel), etc., but really, the lack if a proper keyboard would be my main gripe.
Next on my list would be a number of hardware alterations (I know, these have little to do with iOS 7, but in my opinion, they are well overdue), including a 5" screen (no, not just taller!), powerful Stereo speakers (such as those in an HTC One), waterproofing (Liquipel / HZO / NeverWet), 128GB storage and a decidedly improved battery life (enough to get one through two days of non-stop navigation app use. I know, we'll have to wait for this one at least 10 years). And - should it at all be possible, a much larger / more light-sensitive sensor (this one I wouldn't expect to materialise before half a century from now).