BW does little more than fight in IM2, whereas Whedon actually develops her character. You might not like what he did, but trying to say it was all Theroux is bullshit.
You're forgetting who you are arguing with here, you can cite every instance of Whedon's career where he's written elements similar to those in Avengers film. According to Allen, Whedon couldn't possibly have been involved as a significant contributor to the collaborative process, or it would have failed. You can cite hundreds of similar instances of similar character development, structure, redemptive moments, dialog, group interactions, strong female characters both supporting and leads, whatever you do it won't matter, it just won't matter.
Allen hates Whedon.
If The Avengers failed it would have been Whedon's fault.
If the Avengers succeeded, Whedon had nothing to do with it.
No matter what happened, Whedon was going to be the bad guy, his motivation for even being there were sinister. And it will all be justified with seemingly insider info, or things he "sees" that are obvious to Allen.