I can't speak about Joss Whedon's projects in general since I've only seen Firefly, of his TV work, so I'm gonna stick solely to Age of Ultron, which I saw again yesterday and now feel I have a better handle on.
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I think most of the accusations that AoU had an unfeminist portrayal of Natasha comes from the scene at the farmhouse. Bruce calls himself a monster and Natasha confides in him about the Red Room and graduation ceremony she was subjected to when she was younger. She delivers a line to the effect of "They sterilized us. Turns out it makes a lot of things easier, even killing. Still think you're the only monster here?". That line has been interpreted as Natasha calling herself a "monster" because she can't have children, which would indeed be rather sexist. A woman's ability to bear children is not what gives her worth. However, that's not what Natasha is saying. She is saying that indiscriminate killing as an assassin in the past makes her consider herself a monster. The clumsiness of the dialogue makes it possible to initially read it the other way. Now, I still think the Bruce/Natasha romance makes no sense in the context of the MCU, but is it sexist? My opinion is no. Anyway, it's very likely the the Russos and other MCU directors will ignore the relationship now that Joss is no longer involved in the universe.
All things die, Anakin Skywalker, even stars burn out.
So this is how liberty dies....with thunderous applause.
Those without swords can still die upon them
The world is a mess and I just need to rule it.