Whedon was relatively hands on. Story choices, script notes, etc. Everything went through Whedon, since he was in charge of the Avengers, and Feige, since he's in charge of... everything. Went through more hands than that, too... but Season 1 was considered pretty important for Marvel's TV ambitions, so a lot of hands at Disney and Marvel were on deck to approve of and/or provide suggestions for pretty much every creative decision, even down to the small ones.

Which I think is apparent at times during that season (and, ultimately, why my friend decided to pursue less corporate pastures for Season 2).