Sorry I don't agree that this was more Whedon's movie, watch AOU and then watch Serenity, sure there is the odd similarity like the humour. But in Serenity you don't have people making jokes and quips seconds after a main character dies. But it IS something that is in many MCU movies.
Personality wise Ultron was Whedon, but not a typical Whedon bad guy, look at The Operative, he was dark, serious and a big, big threat to the crew. Ultron was typical MCU movie villain, underdeveloped, doesn't come across as a threat to the heroes and doesn't do anything particularly dark beyond the stand MCU 'wants to destroy the world/universe' motivation. The action was much more brutal in Serenity as well as characters getting really serious moments even when no one had died. Also the upbeat ending despite what had gone on before is nothing like Serenity either.
There is more but I just can't think of them at the moment. There were a lot of many MCU staples in the movie and then also having to set up the next few movies and introduce characters that Marvel demanded.