I'm mainly referring to what a lot of other reviewers said regarding it having a lot of great ideas that are not executed to the best of their abilities. I would have liked to seen a lot of the themes explored more, that's all. The first one that comes to mind is Ultron. It's not just a matter of him not being threatening enough, but also a lot of the philosophy that comes with the character is simplified. Next up would probably be the Twins, who I feel should have at least had a talk with Tony over their past incident.
And honestly, it might just simply be a case of the film trying to have its cake and eat it too. The problem with Ultron is that he's an inherently personal villain, and not exactly the best choice when you're telling a "the team as you know it kicking ***" type of story. Even in the comics, the best Ultron stories often have a primary protagonist the rest of the story centers or (usually Hank or Janet). In this Tony creates Ultron, and has a few moments with him here and there, but it's still ultimately a team film where everyone gets equal treatment (I know I complained the first time it was too Tony-driven, but I changed my mind on that after viewing it a second time). I think someone like Loki or Kang or the Masters of Evil would have been better fit for this particular story.
That's another problem the film has; it feels like it's Whedon's fanfiction Avengers film that he wrote years ago and finally got a chance to adapt. Except that when he finally got the chance to make it, he forgot to take in other factors like continuity and what he can explore here that can't be explored anywhere else. Not having the film so team-focused, for example, wouldn't be a problem an alternate continuity like 616 where that's already been done. Even Quicksilver and Scarlet Witch, as much as I liked them, I don't think were as necessary to the story we got the film tried to makes us believe. I honestly think you could have cut them out with minor script changes and used that time more on Ultron.
Also, by "MCU's best" I really meant "up there with the big four". I have a tendency to go on and on when I type and noticed it seems to discourage a lot of hypesters from replying, particularly when I go on tangents, so I'm trying to minimize things to the main point as much as possible.