I'm looking through the top free iPhone apps in Germany and I can't see a clear trend. Also, I'm not sure how to prove or disprove my point - because being a top app is orthogonal to looking like an amateur effort. WhatsApp has long been #1 here, and while I welcome its stock navigation UI for usability reasons, I think their tacked-on timestamps are as "amateur" as their name.
Some of the UIs are badly imitating UIKit, like Zoosk. They still often replicate the navigation concepts, UIKit shadows (skeuomorphism), widget sizes … - I don't think the stock look & feel is dead yet.
By "amateur" I mean that I think the typical app consumer is getting pretty good at spotting stock UI and tends to equate that with a slapdash app, justified or not.
I think you're misunderstanding. Of your examples, all of them use stock widgets, except for the last two.
In the last two they replaced stock controls with custom ones, even where they didn't have to, and that supports your hypothesis.
But all of the others, however, are using stock controls for all the controls where there is a stock control, and only using custom controls where there is no stock control.
The ability to customize the stock controls has increased a fair bit and gotten more popular as its gotten easier. But these developers (at least, I can't speak for the whole appstore) are using the standard controls.
What is true is that they aren't using the blue-pinstripe look of the original iPhone anymore.
The reason this distinction is important is that its a whole lot harder to do a custom control (like a turntable) than it is to use a standard control, and its also very easy to take that standard control and make it just the right shade of grey, or make it look like wood, etc.
Thus customizing how these standard controls look has gone up dramatically, yes.
What is true is that they aren't using the blue-pinstripe look of the original iPhone anymore.
That's what I mean and that's why I don't think people should waste so much time trying to emulate that look down to the last pixel in Phonegap apps. Users don't care anyway as long as your app looks good.
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http://www.appannie.com/app/ios/camera/
http://www.appannie.com/app/ios/instaframe-pro-photo-frame/
http://www.appannie.com/app/ios/djay-for-iphone-ipod-touch-s...
http://www.appannie.com/app/ios/motionx-gps-drive/
http://www.appannie.com/app/ios/nick-jr-draw-play/