I don't quite agree with that Ars Technica article, or with whatever they're insinuating anyway.
Let's start with the basics. Several applications have always been part of the GApps and not part of AOSP. This includes gmail, talk, maps, etc...
Over time these were updated and changed such that they can be updated through the store rather than requiring a new version of GApps, which is usually supplied with a ROM. So that's an improvement. Closed source stuff remained closed source but it now can be updated easily on devices.
Now moving onto AOSP apps. Calendar, keyboard, messaging, gallery, camera, browser, etc. Ever since android skins have existed (I'm thinking of Sense 2 on the HTC Hero) all of the above apps have been gathered from AOSP, skinned, and included as OEM-exclusive applications. Almost no one gave the user the plain AOSP version of any of those apps. HTC IME keyboard was vastly superior to what AOSP had for example and the browser and calendar both had tweaks and features which wouldn't be available on the Nexus One released much later with stock Android.
So apps in AOSP are barebone versions of the apps. They work but aren't polished and in most cases it is expected that they will be replaced or modified by the OEM.
At this point I'd assume that Google sees that there is no point in fixing or updating AOSP apps because:
a) OEMs will still modify them anyway
b) The more changes in AOSP the harder it'll be for OEMs to update their firmware and release timely updates
c) What is even the point of updating apps which are not to be distributed on the play store and therefore are essentially usable on Nexus devices?
d) Even open communities like CyanogenMod were modifying and rebuilding AOSP apps
So they fork off AOSP and build their own apps, tweak them and release them for all users on the play store. AOSP still has the barebones versions of each of the apps mentioned in the article and are still open source. It's just that for meaningful updates, Google is distributing them through the play store. Ars technica seems to suggest that the only fair thing for Google to do is to have only the Nexus devices running on inferior versions of apps since every OEM will get whatever the Nexus device have and be able to build upon it. At the same time OEM devices have no method of getting the vanilla version of any app because they're only available through AOSP. Sounds silly.
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Handtec listing:
http://www.handtec.co.uk/lg-google-nexus-5-black-16gb.html