I'm hearing-reading that the 3D was greatly improved from that horrendously flat theatrical presentation.
The 3D on the blu-ray is definitely the real deal. The only moment I really recall looking awesome in 3D in the theater was when the Vision flew through the debris to rescue Scarlet Witch. But at home watching a few minutes here and there I'm finding myself amazed pretty much throughout. Like when Hawkeye is recovering on the table in the tower, you see Stark WAY in the background through all those glass walls. Incredible depth. Iron Legion battle after the party looked great too.
The aftermath discussion about Ultron is definitely an awkward scene though. For one, Maria Hill. I get that if you look carefully she appears to be using tweezers to pluck glass shards out of her bare foot but did not one person editing the movie not notice that it looks exactly like she's sitting there clipping her toenails??
How can we really invest in the gravity of that scene if everyone is freaking out about what Ultron is going to do but one person is so relaxed she's openly clipping her toenails in front of everyone. "Oh yeah," *clip clip* "the nuclear codes..." *clip clip* I'm sorry but every time that scene begins I'm like "What the hell? Oh, yeah, that's not what she's doing."
And then there's Thor. Totally contrived moment where he lifts Stark up by the neck. I didn't like it in the theater and still don't. Seems like it was ONLY inserted just to have a "whoa!" moment for the trailer. He arrives, seemingly lifts Stark in a rage, then casually puts him down like nothing happened and they go about their conversation. Just not well done.
But really those are just little things, and even the awkwardness of those weaker moments is kind of amusing. I love this movie.