Umm... You read the first sentence of my post and completely ignored the rest.
Messaging?
Launcher?
Calendar?
Email? (AOSP version of the app crashes when the IMAP server does not have calendar info - WTF?)
Music player?
Browser? How did something that FCs on Settings->General make it out the door?
These are all cases of applications within AOSP where Google started work on a proprietary version of the app and abandoned work on the open-source component. With the exception of Browser, the move was not due to security reasons.
I can understand the desire to integrate Google's services, but the fact that inevitably the open-source non-integrated application gets abandoned is where all of this "AOSP is becoming more closed" sentiment comes from.
At least Google seems to have done it right with Keyboard, where IIRC (I can't check now, so I could be wrong in my memory of this) the AOSP version gains all of the features of the GMS version if a certain native library from GMS is present, but gracefully degrades by simply not offering certain features if it's not present, with the remainder of the keyboard app behaving identically to the GMS variant.