Google Maps will go, perhaps YouTube next?
I think with multiple leaks and confirmation from WSJ Apple doing their own maps is a done deal.
But what if dropping Google Maps is just a part of de-googlifying effort in iOS 6? People often forget that iOS has always had at least 3 Google services built in: Search, Maps and YouTube. I don't see them dropping search any time soon (even though they added Bing some time ago), but YouTube is another likely candidate to be booted from the platform.
Of course, this is just my speculation, but we already saw evidence that Mountain Lion would drop support for uploading videos to YouTube in favor of Vimeo. With iOS 6 and ML going hand-in-hand, it's likely that the former will do the same.
However, knowing how popular are iOS devices for uploading to YouTube, Apple won't leave their users in the cold. Gruber already dropped a hint that iOS 6 might see a system-wide API for data sharing across different apps, similar to 'intents' in Android or 'charms' in Windows 8. Most likely this feature will be presented in the UI as a recognizable arrow button:
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So this will enable Google to release a standalone YouTube app that adds uploading option to the videos' sharing menu. Considering how terrible the current built-in app is (it hasn't been updated since iOS 3 or 4), this would only be a good thing.
EDIT: After thinking about this a bit more, it occurred to me: what current YouTube app doesn't have?
ADS! Neither banners, nor overlays, nor video pre-roll ads that are ubiquitous on their desktop site. Considering how popular iOS devices are for watching YouTube (especially iPads), it's not a question of 'if', but 'when' Google will decide to put ads in the app as well. But since the current app is developed by Apple and is baked into OS, it's not easy for Google to implement ads if they don't have control over it.
So most likely Apple and Google will negotiate a deal, with Apple dropping YouTube app from iOS but in exchange letting Google to build their own with ads, and publish it on the App Store.