Well keep in mind, he's playing in the Marvel sandbox with characters he doesn't really 'own'. Unless he brings some new ones that he personally created in one of his own runs writing for Marvel, then he can't really dick around too much with the way the tentpole characters are written. Now that said, I do forsee Avengers being a bit darker - simply because of what we already know about Iron Man 3 where Tony really just 'into' the whole super hero thing and the others sort of are hesitant to come back, so maybe I can see the first act or so being incredibly dark and depressing. But then it picks up toward the 2nd and 3rd act and hits the right 'fun' 'quirky' Whedon-esque notes.
I would really love to see more of Cap struggling with 21st Century life. I mean let's be honest, things aren't THAT different between how Cap was in the 40s to how he was in 2012, I mean he was still in a military setting with SHIELD, he was still fighting a war against powerfully armed bad guys. He was still part of a unit. Not much was really all that different. Sure there was more tech, sure there's a different 'feel' to things, but I'd like to see him, having had months (or even a couple of years) to get used to 21st Century life and see him sort of struggle with it. I mean would Captain America carry a cell phone? Would he play video games - lol be a hoot to see him playing Call of Duty and bitching all the while. 'Oh that's not how it was like AT ALL. Those lugers have far less range than that.'
I COULD see Hawkeye maybe changing personality-wise. I would love to see him be more like the Hawkeye from the comics, a bit arrogant, jerky, snarky and kind of funny. Maybe as a mask to hide his PTSD.
I COULD see Bruce still struggling with the Hulk side of things - sure he's got some measure of control, but Hulk is still a challenge to control when he's Hulked out. I mean everyone forgets that he DID smash up the SHIELD helicarrier and stalked Black Widow through the ship, fully intending to 'smash' her. So Bruce is far from having complete control of the Hulk. Sure in the last act, it seemed like that finally happened. But its tenuous at best. Sure he can control the transformation, but it's getting the Hulk himself to behave that's the trick.
Tony will be Tony - he'll go between being this great, fun guy to a total douchenozzle and back again. It's his 'thing'.