Really, his recognition of Thor's change (which waited over halfway through the series) seemed to validate Millar's version as a better one. The Hippie-Thor robot made fun of Thor's Old English speech. If anything, Loeb's Thor became a self-parody.
But other than Thor and Cap, I'm really not seeing anything. I guess you could throw the Pietro/Wanda relationship and Tony's alcoholism in there as well. And if you stretched, Jan and Hank's relationship, too. But it really just comes across as face-value interpretations of Millar's characters.
If the point was to deconstruct Millar's Ultimates, why was there so much new stuff thrown in that had nothing to do with that purpose? What was the point of adding Valkyrie's powers or Cap as Black Panther? And what do the one-liners and over-the-top violence have to do with anything?
In regards to your first post, I can tell you, without a shadow of a doubt, that Ultimates 3 is not disliked because it points out flaws in Millar's work. I've read all three volumes several times, and I still don't see these apparent flaws. I can see things that would stop some people from liking the books, but I see that in every comic I've ever read; that's not a flaw. If Loeb's aim was to point out Millar's flaws, he did a terrible job at it.