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You gotta love the casual reveal that A. SHIELD has known where Bruce Banner is all along, B. They've been leaving him alone, and C. Actually protecting him, presumably from other branches of the US military that would swoop in, make him Hulk out, and end up just fucking things up for everybody. Given that the classic Hulk pathos is "Why don't they just leave him alone?", the fact that SHIELD does makes for the first time in recent memory that the protagonists (or at least Nick Fury) are dangerously genre savvy.
And I'm sure there'll be fans who are disappointed by Hawkeye spending a lot of the movie as Loki's buttmonkey, but it's not a case of him getting X2ed a la Cyclops. Comparing those two movies, you see a lot of smarts on the part of Whedon, and laziness on the part of the X2 writers.
1. Although Hawkeye isn't "himself," we are getting to see him in action and what a badass he is, which is more similar to Nightcrawler in X2 than Cyclops. He doesn't just disappear for most of the movie. The mind control is actually a really cool way of showing him off while avoiding him getting lost in the tangle of SHIELD agents.
2. Instead of Jean Gray ignoring her endangered beau to mack on Wolverine, Natasha cares deeply about Hawkeye and the situation sheds maybe more light on their relationship than if they were just in action together. In fact, what was the Scott/Jean situation in the X-Men movies? Were they married? Engaged? Dating?