Well, we're in somewhat uncharted territories with this whole cinematic universe thing. Many film critics will insist that each movie most be considered and evaluated purely on its own content, not taking into account the rest of their series. The San Francisco Chronicle's Mick Lasalle, for example, gave The Hunger Games: Mockingjay Part I a terrible review on the basis that it didn't tell a full story. He knew full well the filmmakers only intended to tell half a story, of course, but he didn't care, and rated the movie as though there would be no Part II. I don't fully agree with that reasoning, but he's consistent about it, so I respect his stance.
By that line of thinking, Whedon had zero responsibility to fill in the gaps between his movie and the end of IM3. You're saying he had full responsibility. Myself, I fall a bit in the middle. I would have liked to see AoU open with a half-hour of character introductions again, picking up each Avenger's story from where they left off and showing them assemble once more, but Whedon was obviously more interested in telling his Ultron story, which he'd wanted to do since the first movie. I didn't find said story very compelling, but that was clearly his/the movie's aim.
Personally, I get the impression that each film is given a certain amount of free story telling and a certain amount of required setup and IM3 very crucially screwed up that balance. Every source seems to indicate that Iron Man was always supposed to remain Iron Man, yet the amount of confusion on the subject makes it very clear that the ending as written did a piss poor job of conveying that.
Personally I really liked that this movie started already fully in motion and we didn't have to sit around waiting for the band to get back together again before the story could start, so from that pov, I'm more inclined to blame IM3 for this particular plot hole than AOU. Especially since - with the ridiculous amount of setup already packed into this film - I'm not sure it would've been fair to turn around and say they also have to alter the story to explicitly clarify IM3's poor ending as well.
On the other hand, I can understand if someone says that since the other movie failed to convey the idea, it needed to be addressed, period. I suppose it all comes down to what is more important in your eyes - smoothing over continuity problems between films or allowing individual films to tell their own story unburdened by the mistakes made in previous films.
That's an interesting thought, but I still blame Avengers 2 because IM3 (which I recall being well-received), set it up for Avengers 2, and so it was up to Avengers 2 to take the ball and run with it.
Otherwise, why make it the MCU? Why all the care and attention to detail in connecting these stories in the MCU? Just to be able to switch it off for Avengers 2?
You could have started Avengers 2 precisely as it did, with a great action sequence, but involve War Machine and have your "Safe House scene" involve returning Tony Stark to the action. Or maybe you could have Tony Stark earlier, but in a more advisory capacity.
It doesn't have to be a drawn out thing, but Stark walking away was a definite major development for Stark (again, the friggin' star of the whole damn franchise), and to have it virtually ignored seemed careless and sloppy.
But as I mentioned before, Tony Stark isn't the only character that somehow devolved. He just happens to stick out like a sore thumb because he is the star of the MCU and IM3 was very well received .
The difference between IM3 and A2 is quite glaring, making me feel that IM3 was expendable and meaningless. Whether you blame IM3 or Avengers 2, doesn't matter, because either way, it's a slight kink in MCU's armor, which was ironclad until now.
Once again, to clarify: I liked the movie overall, but the franchise is now showing some vulnerability for the first time in a long time.
In fact, I wold say MCU: Phase II was damn near flawless: IM3, Thor 2, Captain America 2, Guardians of the Galaxy---there's very little way I think those movies could be any better executed than they were. FLAWLESSLY executed...until it's climax in Avengers 2.
Unfortunately.