The author of this article makes some naïve assumptions about modern auto-tune systems, including but not limited to Antares Auto-Tune. His primary mistaken assumption is that an auto-tune system will snap a note perfectly into alignment with an ideal pitch. This is not true. A sophisticated automated system (like Antares Auto-Tune, in typical usage, not for the Cher effect) uses heuristics to find a more natural, imperfect pitch to use as an alignment.

And this is just for "fire and forget" auto-tune. If you work an auto-tune by hand – and most skilled engineers will do this, when it's called for – you can use your own judgment as a musician to figure out what to do. Antares Auto-Tune lets you do this by presenting a sort of X-Y plot of pitch over time which you can manipulate. Melodyne does something similar, with a little more sophistication (it actually pioneered this technique.)

Another one of his incorrect assumptions is that auto-tune still behaves like that patent from 1998. While some of the algorithms involved are the same, the systems of today [1] use lookahead on the audio source, so that the pitch correction isn't constantly playing 'catchup' (it takes at least a coupe of cycles of an oscillating wave to determine its pitch with reasonable accuracy.) So you would not see something start wrong and then deviate towards its ideal pitch – in fact, you might see it start too accurately.

The primary destruction auto-tune wreaks on vocal performances isn't just too-perfect pitch: it destroys the subtly and intonation that good performers can impart. A real vocalist doesn't hit the ideal pitch at the start of each note, because it's hard to make the human voice do that. They use the imperfection to their advantage. There's a lot of subtle complexity that auto-tune can just wipe out when you use it.

Of course, if the vocalist isn't that good, then there's not any real loss.

As for his article, even assuming the methods he used to analyze the songs were not based on a misconception, the resolution is too low. Perhaps surprisingly, the human ear is capable of distinguishing pitch much more finely than the graphs he plotted.

Edited addendum: here are a couple of screenshots of the actual Antares Auto-Tune software that will illustrate what I'm talking about.

Here is a picture of the Auto-Tune software set in fire-and-forget 'auto' mode. http://www.antarestech.com/images/ATEvo_Auto_mode.jpg

Notice the prominent 'Retune Speed' adjustment knob. This is how you used it in the late 90s and early 00s, or today when you want the robot or Cher effect.

Now here is a picture of Auto-Tune in use in Graphical mode, where you adjust the pitches directly. This is how most engineers today will use Auto-Tune when it's not for a deliberate, noticeable effect. http://www.antarestech.com/images/ATEvo_Graphic_full.jpg

Notice there is no retune speed adjustment knob. Instead, you edit the pitches directly in a graph.

[1] In a non-live-performance setting, anyway. It introduces latency, so if you used this live, it would add 'lag' to the performer's input. Bad.